rs956642

Variant names:

• chr7-150899414-G-A
• rs956642
• ENST00000726373.1:n.221+1981C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-150899414-G-A
• chr7-150899414-G-C

Variant summary

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

The ENST00000726373.1(ENSG00000289052):​n.221+1981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,802 control chromosomes in the GnomAD database, including 31,875 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 0.64 (31875 hom., cov: 29)
• Consequence: ENSG00000289052 ENST00000726373.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 6 publications found

Genes affected

ENSG00000289052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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
ENSG00000289052	ENST00000726373.1	n.221+1981C>T		intron_variant	Intron 1 of 1
ENSG00000289052	ENST00000726378.1	n.246-610C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97754 AN: 151682 Hom.: 31846 Cov.: 29

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.645 AC: 97840 AN: 151802 Hom.: 31875 Cov.: 29 AF XY: 0.641 AC XY: 47557 AN XY: 74156

African (AFR) AF: 0.739 AC: 30558 AN: 41368

American (AMR) AF: 0.620 AC: 9463 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2221 AN: 3466

East Asian (EAS) AF: 0.683 AC: 3514 AN: 5142

South Asian (SAS) AF: 0.716 AC: 3435 AN: 4796

European-Finnish (FIN) AF: 0.539 AC: 5674 AN: 10522

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40945 AN: 67930

Other (OTH) AF: 0.625 AC: 1314 AN: 2102

Alfa AF: 0.615 Hom.: 6681

Bravo AF: 0.653

Asia WGS AF: 0.645 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs956642; hg19: chr7-150596502; COSMIC: COSV70648370;