rs7751725

chr6-31392656-A-Gchr6-31392656-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 0.311 in 151,622 control chromosomes in the GnomAD database, including 7,975 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 0.31 (7975 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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 (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47095 AN: 151504 Hom.: 7961 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.311 AC: 47153 AN: 151622 Hom.: 7975 Cov.: 31 AF XY: 0.316 AC XY: 23413 AN XY: 74090

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.326

Alfa AF: 0.270 Hom.: 2847

Bravo AF: 0.315

Asia WGS AF: 0.316 AC: 1099 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7751725; hg19: chr6-31360433; COSMIC: COSV74094117;