7-116801535-A-G

Variant names:

• chr7-116801535-A-G
• rs42336

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.351 in 152,104 control chromosomes in the GnomAD database, including 11,179 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 0.35 (11179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.352 AC: 53440 AN: 151986 Hom.: 11192 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.351 AC: 53414 AN: 152104 Hom.: 11179 Cov.: 32 AF XY: 0.353 AC XY: 26277 AN XY: 74348

African (AFR) AF: 0.105 AC: 4371 AN: 41536

American (AMR) AF: 0.445 AC: 6803 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3470

East Asian (EAS) AF: 0.470 AC: 2439 AN: 5184

South Asian (SAS) AF: 0.457 AC: 2199 AN: 4816

European-Finnish (FIN) AF: 0.381 AC: 4022 AN: 10558

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30673 AN: 67958

Other (OTH) AF: 0.387 AC: 815 AN: 2104

Alfa AF: 0.397 Hom.: 2708

Bravo AF: 0.346

Asia WGS AF: 0.415 AC: 1441 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	22
DANN	Benign	0.82
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs42336; hg19: chr7-116441589;