rs9892622

Variant names:

• chr17-78350041-G-A
• rs9892622
• ENST00000794841.1:n.139-4438C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-78350041-G-A
• chr17-78350041-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000794841.1(ENSG00000303469):​n.139-4438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,000 control chromosomes in the GnomAD database, including 20,397 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 0.50 (20397 hom., cov: 31)
• Consequence: ENSG00000303469 ENST00000794841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 7 publications found

Genes affected

ENSG00000303469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

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
ENSG00000303469	ENST00000794841.1	n.139-4438C>T		intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794842.1	n.135+3362C>T		intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794843.1	n.212+2395C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76712 AN: 151882 Hom.: 20395 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.505 AC: 76735 AN: 152000 Hom.: 20397 Cov.: 31 AF XY: 0.508 AC XY: 37721 AN XY: 74294

African (AFR) AF: 0.326 AC: 13499 AN: 41462

American (AMR) AF: 0.576 AC: 8803 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3006 AN: 5168

South Asian (SAS) AF: 0.556 AC: 2679 AN: 4816

European-Finnish (FIN) AF: 0.602 AC: 6369 AN: 10580

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39020 AN: 67926

Other (OTH) AF: 0.509 AC: 1074 AN: 2108

Alfa AF: 0.545 Hom.: 29855

Bravo AF: 0.494

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.3
DANN	Benign	0.75
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs9892622; hg19: chr17-76346122;