rs10923844

Variant names:

• chr1-119516877-G-A
• rs10923844
• ENST00000632456.2:n.243-26765C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-119516877-G-A
• chr1-119516877-G-C
• chr1-119516877-G-T

Variant summary

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

The ENST00000756941.1(ENSG00000293080):​n.219-31269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,840 control chromosomes in the GnomAD database, including 29,803 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 0.61 (29803 hom., cov: 31)
• Consequence: ENSG00000293080 ENST00000756941.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 7 publications found

Genes affected

ENSG00000293080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756941.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293080	ENST00000632456.2	TSL:6	n.243-26765C>T		intron	N/A
	ENSG00000293080	ENST00000756941.1		n.219-31269C>T		intron	N/A
	ENSG00000293080	ENST00000756942.1		n.259-26765C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91929 AN: 151724 Hom.: 29799 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.606 AC: 91952 AN: 151840 Hom.: 29803 Cov.: 31 AF XY: 0.616 AC XY: 45724 AN XY: 74180

African (AFR) AF: 0.358 AC: 14817 AN: 41362

American (AMR) AF: 0.710 AC: 10831 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2305 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4488 AN: 5108

South Asian (SAS) AF: 0.769 AC: 3703 AN: 4814

European-Finnish (FIN) AF: 0.743 AC: 7854 AN: 10564

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45742 AN: 67952

Other (OTH) AF: 0.617 AC: 1296 AN: 2102

Alfa AF: 0.625 Hom.: 12587

Bravo AF: 0.590

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
DANN	Benign	0.55
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10923844; hg19: chr1-120059500; COSMIC: COSV52489955;