7-113094238-G-A

Variant names:

• chr7-113094238-G-A
• rs7778565

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 0.0562 in 151,972 control chromosomes in the GnomAD database, including 297 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 0.056 (297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 8532 AN: 151854 Hom.: 295 Cov.: 32

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0595

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0494

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

GnomAD4 genome AF: 0.0562 AC: 8536 AN: 151972 Hom.: 297 Cov.: 32 AF XY: 0.0579 AC XY: 4304 AN XY: 74288

African (AFR) AF: 0.0272 AC: 1129 AN: 41498

American (AMR) AF: 0.0371 AC: 566 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0595 AC: 206 AN: 3464

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5166

South Asian (SAS) AF: 0.131 AC: 633 AN: 4822

European-Finnish (FIN) AF: 0.0771 AC: 814 AN: 10564

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0699 AC: 4749 AN: 67908

Other (OTH) AF: 0.0489 AC: 103 AN: 2108

Alfa AF: 0.0507 Hom.: 97

Bravo AF: 0.0503

Asia WGS AF: 0.0850 AC: 296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.26
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7778565; hg19: chr7-112734293;