chr7-108670542-A-G

Variant names:

• chr7-108670542-A-G
• rs193451

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 0.352 in 152,044 control chromosomes in the GnomAD database, including 10,056 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 (10056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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: 0.352 AC: 53515 AN: 151926 Hom.: 10048 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.352 AC: 53547 AN: 152044 Hom.: 10056 Cov.: 32 AF XY: 0.347 AC XY: 25808 AN XY: 74310

African (AFR) AF: 0.283 AC: 11734 AN: 41464

American (AMR) AF: 0.397 AC: 6070 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.0427 AC: 221 AN: 5176

South Asian (SAS) AF: 0.287 AC: 1377 AN: 4802

European-Finnish (FIN) AF: 0.359 AC: 3798 AN: 10566

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28236 AN: 67962

Other (OTH) AF: 0.332 AC: 702 AN: 2116

Alfa AF: 0.271 Hom.: 3050

Bravo AF: 0.347

Asia WGS AF: 0.171 AC: 597 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	4.3
DANN	Benign	0.74
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs193451; hg19: chr7-108310986;