rs7801876

Variant names:

• chr7-117962072-A-G
• rs7801876

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.300 AC: 12428 AN: 41462

American (AMR) AF: 0.302 AC: 4613 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1274 AN: 3466

East Asian (EAS) AF: 0.110 AC: 565 AN: 5152

South Asian (SAS) AF: 0.417 AC: 2005 AN: 4810

European-Finnish (FIN) AF: 0.551 AC: 5822 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29352 AN: 67938

Other (OTH) AF: 0.352 AC: 744 AN: 2114

Alfa AF: 0.422 Hom.: 7152

Bravo AF: 0.347

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.84
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7801876; hg19: chr7-117602126;