rs2903813

Variant names:

• chr7-76301472-A-G
• rs2903813

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 0.155 in 151,880 control chromosomes in the GnomAD database, including 2,049 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 0.16 (2049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 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: 0.155 AC: 23599 AN: 151764 Hom.: 2050 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.155 AC: 23597 AN: 151880 Hom.: 2049 Cov.: 32 AF XY: 0.159 AC XY: 11770 AN XY: 74174

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0968

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.137

Alfa AF: 0.161 Hom.: 3215

Bravo AF: 0.148

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2903813; hg19: chr7-75930789;