chr7-157087704-A-G

Variant names:

• chr7-157087704-A-G
• rs6966038

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 0.267 in 152,060 control chromosomes in the GnomAD database, including 6,868 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 0.27 (6868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.266 AC: 40492 AN: 151942 Hom.: 6856 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.267 AC: 40543 AN: 152060 Hom.: 6868 Cov.: 32 AF XY: 0.263 AC XY: 19561 AN XY: 74340

African (AFR) AF: 0.496 AC: 20551 AN: 41452

American (AMR) AF: 0.179 AC: 2729 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3470

East Asian (EAS) AF: 0.0483 AC: 250 AN: 5176

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4804

European-Finnish (FIN) AF: 0.193 AC: 2041 AN: 10588

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12519 AN: 67984

Other (OTH) AF: 0.222 AC: 469 AN: 2108

Alfa AF: 0.204 Hom.: 14431

Bravo AF: 0.275

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6966038; hg19: chr7-156880398;