rs2868371

Variant names:

• chr7-76301442-C-G
• rs2868371

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 0.224 in 152,000 control chromosomes in the GnomAD database, including 4,511 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 0.22 (4511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 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: 0.224 AC: 34040 AN: 151882 Hom.: 4508 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.224 AC: 34053 AN: 152000 Hom.: 4511 Cov.: 32 AF XY: 0.227 AC XY: 16863 AN XY: 74272

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.230

Alfa AF: 0.229 Hom.: 520

Bravo AF: 0.228

Asia WGS AF: 0.415 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2868371; hg19: chr7-75930759;