19-57456271-TAA-T

Variant names:

• chr19-57456271-TAA-T
• rs200574657
• NM_020633.4:c.214_215delTT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_020633.4(VN1R1):​c.214_215delTT​(p.Leu72AsnfsTer22) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,613,594 control chromosomes in the GnomAD database, including 42 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0095 (27 hom., cov: 32)
  • Exomes 𝑓: 0.00099 (15 hom.)
• Consequence: VN1R1 NM_020633.4 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.534
• Publications: 0 publications found

Genes affected

VN1R1 (HGNC:13548): (vomeronasal 1 receptor 1) Pheromones are chemical signals that elicit specific behavioral responses and physiologic alterations in recipients of the same species. The protein encoded by this gene is similar to pheromone receptors and is primarily localized to the olfactory mucosa. An alternate splice variant of this gene is thought to exist, but its full length nature has not been determined. [provided by RefSeq, Jul 2008]

ENSG00000268163 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 19-57456271-TAA-T is Benign according to our data. Variant chr19-57456271-TAA-T is described in ClinVar as Benign. ClinVar VariationId is 712016.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00947 (1442/152256) while in subpopulation AFR AF = 0.0327 (1359/41538). AF 95% confidence interval is 0.0313. There are 27 homozygotes in GnomAd4. There are 683 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 27 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020633.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VN1R1	NM_020633.4	MANE Select	c.214_215delTT	p.Leu72AsnfsTer22	frameshift	Exon 1 of 1	NP_065684.1	Q9GZP7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VN1R1	ENST00000321039.5	TSL:6 MANE Select	c.214_215delTT	p.Leu72AsnfsTer22	frameshift	Exon 1 of 1	ENSP00000322339.3	Q9GZP7
	ENSG00000268163	ENST00000596831.1	TSL:2	c.200-91_200-90delTT		intron	N/A	ENSP00000470969.1	M0R036
	ENSG00000268163	ENST00000415705.3	TSL:2	n.300-91_300-90delTT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00946 AC: 1439 AN: 152140 Hom.: 27 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00373

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00717

GnomAD2 exomes AF: 0.00259 AC: 650 AN: 250884 AF XY: 0.00183

Gnomad AFR exome AF: 0.0331

Gnomad AMR exome AF: 0.00209

Gnomad ASJ exome AF: 0.0000995

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000256

Gnomad OTH exome AF: 0.00164

GnomAD4 exome AF: 0.000987 AC: 1443 AN: 1461338 Hom.: 15 AF XY: 0.000872 AC XY: 634 AN XY: 726942

African (AFR) AF: 0.0307 AC: 1024 AN: 33398

American (AMR) AF: 0.00258 AC: 115 AN: 44630

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26118

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39688

South Asian (SAS) AF: 0.0000232 AC: 2 AN: 86188

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.00277 AC: 16 AN: 5766

European-Non Finnish (NFE) AF: 0.000159 AC: 177 AN: 1111766

Other (OTH) AF: 0.00179 AC: 108 AN: 60368

GnomAD4 genome AF: 0.00947 AC: 1442 AN: 152256 Hom.: 27 Cov.: 32 AF XY: 0.00917 AC XY: 683 AN XY: 74452

African (AFR) AF: 0.0327 AC: 1359 AN: 41538

American (AMR) AF: 0.00373 AC: 57 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 68014

Other (OTH) AF: 0.00710 AC: 15 AN: 2114

Alfa AF: 0.00515 Hom.: 3

Bravo AF: 0.0110

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.000273

EpiControl AF: 0.000474

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.53
Mutation Taster		=192/8	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs200574657; hg19: chr19-57967639;