rs6972688

Positions:

• chr7-155031239-A-G
• chr7-155031239-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.353

Alfa AF: 0.321 Hom.: 16206

Bravo AF: 0.333

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6972688; hg19: chr7-154822949;