chr7-155031239-A-G

Variant names:

• chr7-155031239-A-G
• rs6972688

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 0.337 in 151,864 control chromosomes in the GnomAD database, including 8,654 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 0.34 (8654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51099 AN: 151748 Hom.: 8619 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.337 AC: 51187 AN: 151864 Hom.: 8654 Cov.: 31 AF XY: 0.341 AC XY: 25270 AN XY: 74192

African (AFR) AF: 0.351 AC: 14550 AN: 41422

American (AMR) AF: 0.329 AC: 5013 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1955 AN: 5166

South Asian (SAS) AF: 0.347 AC: 1663 AN: 4794

European-Finnish (FIN) AF: 0.395 AC: 4150 AN: 10514

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21677 AN: 67938

Other (OTH) AF: 0.353 AC: 744 AN: 2108

Alfa AF: 0.324 Hom.: 25644

Bravo AF: 0.333

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6972688; hg19: chr7-154822949; COSMIC: COSV107155872;