rs7801876

Variant names:

• chr7-117962072-A-G
• rs7801876

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 0.376 in 151,966 control chromosomes in the GnomAD database, including 11,476 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 0.38 (11476 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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: 0.376 AC: 57110 AN: 151848 Hom.: 11484 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.376 AC: 57115 AN: 151966 Hom.: 11476 Cov.: 32 AF XY: 0.381 AC XY: 28319 AN XY: 74276

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.352

Alfa AF: 0.423 Hom.: 6520

Bravo AF: 0.347

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
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: rs7801876; hg19: chr7-117602126;