rs2373124

Variant names:

• chr7-86200956-G-A
• rs2373124
• ENST00000757672.1:n.93-16496C>T

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.93-16496C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,088 control chromosomes in the GnomAD database, including 43,970 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 0.76 (43970 hom., cov: 33)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 4 publications found

Genes affected

ENSG00000298738 (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 (EAS) allele frequency at 95% confidence interval = 0.903 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
ENSG00000298738	ENST00000757672.1	n.93-16496C>T		intron_variant	Intron 1 of 3
ENSG00000298738	ENST00000757673.1	n.92-16496C>T		intron_variant	Intron 1 of 2
ENSG00000298738	ENST00000757674.1	n.92-16496C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115009 AN: 151970 Hom.: 43919 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.757 AC: 115119 AN: 152088 Hom.: 43970 Cov.: 33 AF XY: 0.758 AC XY: 56327 AN XY: 74344

African (AFR) AF: 0.711 AC: 29496 AN: 41458

American (AMR) AF: 0.806 AC: 12319 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2958 AN: 3468

East Asian (EAS) AF: 0.925 AC: 4774 AN: 5162

South Asian (SAS) AF: 0.921 AC: 4449 AN: 4828

European-Finnish (FIN) AF: 0.633 AC: 6697 AN: 10572

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51904 AN: 67996

Other (OTH) AF: 0.787 AC: 1660 AN: 2108

Alfa AF: 0.770 Hom.: 25460

Bravo AF: 0.764

Asia WGS AF: 0.905 AC: 3143 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.31
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs2373124; hg19: chr7-85830272;