rs10461692

Variant names:

• chr5-30938286-G-A
• rs10461692
• ENST00000797583.1:n.122-32700C>T

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.122-32700C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,754 control chromosomes in the GnomAD database, including 6,527 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 0.28 (6527 hom., cov: 31)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 0 publications found

Genes affected

ENSG00000303861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 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
ENSG00000303861	ENST00000797583.1	n.122-32700C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42883 AN: 151634 Hom.: 6524 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.283 AC: 42884 AN: 151754 Hom.: 6527 Cov.: 31 AF XY: 0.281 AC XY: 20857 AN XY: 74154

African (AFR) AF: 0.184 AC: 7636 AN: 41410

American (AMR) AF: 0.235 AC: 3576 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3462

East Asian (EAS) AF: 0.154 AC: 795 AN: 5156

South Asian (SAS) AF: 0.278 AC: 1336 AN: 4808

European-Finnish (FIN) AF: 0.354 AC: 3720 AN: 10504

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23471 AN: 67864

Other (OTH) AF: 0.308 AC: 649 AN: 2106

Alfa AF: 0.319 Hom.: 997

Bravo AF: 0.268

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.62
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10461692; hg19: chr5-30938393;