7-156131242-A-G

Variant names:

• chr7-156131242-A-G
• rs4716990

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 0.355 in 151,954 control chromosomes in the GnomAD database, including 10,278 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 (10278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 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: 0.355 AC: 53882 AN: 151834 Hom.: 10281 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.355 AC: 53899 AN: 151954 Hom.: 10278 Cov.: 32 AF XY: 0.357 AC XY: 26504 AN XY: 74302

African (AFR) AF: 0.468 AC: 19376 AN: 41380

American (AMR) AF: 0.395 AC: 6039 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1956 AN: 5166

South Asian (SAS) AF: 0.488 AC: 2341 AN: 4800

European-Finnish (FIN) AF: 0.239 AC: 2527 AN: 10582

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19261 AN: 67966

Other (OTH) AF: 0.378 AC: 798 AN: 2112

Alfa AF: 0.318 Hom.: 4164

Bravo AF: 0.371

Asia WGS AF: 0.399 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.68
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4716990; hg19: chr7-155923936;