6-15922795-T-C

Variant names:

• chr6-15922795-T-C
• rs16877320
• ENST00000806821.1:n.448+68243T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000806821.1(ENSG00000289953):​n.448+68243T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0372 in 152,350 control chromosomes in the GnomAD database, including 123 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.037 (123 hom., cov: 33)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 10 publications found

Genes affected

ENSG00000289953 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0372 (5661/152350) while in subpopulation NFE AF = 0.0457 (3109/68018). AF 95% confidence interval is 0.0444. There are 123 homozygotes in GnomAd4. There are 2897 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 123 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289953	ENST00000806821.1	n.448+68243T>C		intron_variant	Intron 2 of 3
ENSG00000289953	ENST00000806822.1	n.462+68243T>C		intron_variant	Intron 2 of 3
ENSG00000289953	ENST00000806823.1	n.303-25447T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5651 AN: 152232 Hom.: 122 Cov.: 33

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0287

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0411

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0372 AC: 5661 AN: 152350 Hom.: 123 Cov.: 33 AF XY: 0.0389 AC XY: 2897 AN XY: 74506

African (AFR) AF: 0.0249 AC: 1036 AN: 41590

American (AMR) AF: 0.0287 AC: 439 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.00443 AC: 23 AN: 5192

South Asian (SAS) AF: 0.0304 AC: 147 AN: 4830

European-Finnish (FIN) AF: 0.0688 AC: 731 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0457 AC: 3109 AN: 68018

Other (OTH) AF: 0.0435 AC: 92 AN: 2116

Alfa AF: 0.0210 Hom.: 11

Bravo AF: 0.0338

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.38
DANN	Benign	0.59
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs16877320; hg19: chr6-15923026;