rs10003623

Variant names:

• chr4-60584377-A-G
• rs10003623
• ENST00000843131.1:n.76-13717T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-60584377-A-G
• chr4-60584377-A-T

Variant summary

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

The ENST00000843131.1(ENSG00000309699):​n.76-13717T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,218 control chromosomes in the GnomAD database, including 1,421 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 0.12 (1421 hom., cov: 33)
• Consequence: ENSG00000309699 ENST00000843131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 0 publications found

Genes affected

ENSG00000309699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843131.1. 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
	ENSG00000309699	ENST00000843131.1		n.76-13717T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18854 AN: 152100 Hom.: 1417 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.124 AC: 18879 AN: 152218 Hom.: 1421 Cov.: 33 AF XY: 0.123 AC XY: 9141 AN XY: 74436

African (AFR) AF: 0.215 AC: 8915 AN: 41516

American (AMR) AF: 0.0744 AC: 1137 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3468

East Asian (EAS) AF: 0.103 AC: 534 AN: 5180

South Asian (SAS) AF: 0.128 AC: 617 AN: 4828

European-Finnish (FIN) AF: 0.0862 AC: 915 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0922 AC: 6273 AN: 68002

Other (OTH) AF: 0.103 AC: 217 AN: 2116

Alfa AF: 0.108 Hom.: 264

Bravo AF: 0.126

Asia WGS AF: 0.125 AC: 434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.78
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10003623; hg19: chr4-61450095;