rs2373124

Variant names:

• chr7-86200956-G-A
• rs2373124

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.787

Alfa AF: 0.770 Hom.: 22949

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2373124; hg19: chr7-85830272;