rs10911628

Variant names:

• chr1-184680369-C-A
• rs10911628
• ENST00000717067.1:n.185+146G>T

Variant summary

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

The ENST00000717067.1(ENSG00000285847):​n.185+146G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 152,198 control chromosomes in the GnomAD database, including 852 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 0.092 (852 hom., cov: 32)
• Consequence: ENSG00000285847 ENST00000717067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 8 publications found

Genes affected

ENSG00000285847 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717067.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285847	ENST00000717067.1		n.185+146G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0916 AC: 13928 AN: 152080 Hom.: 851 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0917 AC: 13954 AN: 152198 Hom.: 852 Cov.: 32 AF XY: 0.0880 AC XY: 6548 AN XY: 74402

African (AFR) AF: 0.174 AC: 7246 AN: 41526

American (AMR) AF: 0.0755 AC: 1155 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0874 AC: 303 AN: 3468

East Asian (EAS) AF: 0.0482 AC: 250 AN: 5182

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4824

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0630 AC: 4285 AN: 67998

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.0702 Hom.: 1133

Bravo AF: 0.101

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.61
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10911628; hg19: chr1-184649503;