rs2373816

chr7-150574041-G-Achr7-150574041-G-T

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 0.709 in 152,028 control chromosomes in the GnomAD database, including 39,335 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 0.71 (39334 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107743 AN: 151906 Hom.: 39291 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.709 AC: 107842 AN: 152026 Hom.: 39334 Cov.: 31 AF XY: 0.715 AC XY: 53089 AN XY: 74296

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.648

Alfa AF: 0.649 Hom.: 12619

Bravo AF: 0.711

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.0
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: rs2373816; hg19: chr7-150271129;