rs71992086

Variant names:

• chr9-104317871-TAGACAGACAGAC-T
• rs71992086
• ENST00000745188.1:n.605-113870_605-113859delGTCTGTCTGTCT

Your query was ambiguous. Multiple possible variants found:

• chr9-104317871-TAGACAGACAGAC-T
• chr9-104317871-TAGACAGACAGAC-TAGAC
• chr9-104317871-TAGACAGACAGAC-TAGACAGAC
• chr9-104317871-TAGACAGACAGAC-TAGACAGACAGACAGAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000745188.1(ENSG00000297079):​n.605-113870_605-113859delGTCTGTCTGTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.010 (28 hom., cov: 13)
• Consequence: ENSG00000297079 ENST00000745188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 1 publications found

Genes affected

ENSG00000297079 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0101 (1485/147032) while in subpopulation AFR AF = 0.0364 (1415/38912). AF 95% confidence interval is 0.0348. There are 28 homozygotes in GnomAd4. There are 679 alleles in the male GnomAd4 subpopulation. Median coverage is 13. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 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
ENSG00000297079	ENST00000745188.1	n.605-113870_605-113859delGTCTGTCTGTCT		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1486 AN: 146928 Hom.: 28 Cov.: 13

Gnomad AFR AF: 0.0365

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00315

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000217

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000595

Gnomad OTH AF: 0.00946

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

GnomAD4 genome AF: 0.0101 AC: 1485 AN: 147032 Hom.: 28 Cov.: 13 AF XY: 0.00947 AC XY: 679 AN XY: 71668

African (AFR) AF: 0.0364 AC: 1415 AN: 38912

American (AMR) AF: 0.00315 AC: 46 AN: 14608

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3424

East Asian (EAS) AF: 0.00 AC: 0 AN: 4968

South Asian (SAS) AF: 0.000217 AC: 1 AN: 4598

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10064

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000595 AC: 4 AN: 67232

Other (OTH) AF: 0.00936 AC: 19 AN: 2030

Alfa AF: 0.00 Hom.: 157

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs71992086; hg19: chr9-107080152;