rs6972429

Variant names:

• chr7-41855244-C-T
• rs6972429

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 0.692 in 152,126 control chromosomes in the GnomAD database, including 37,429 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 0.69 (37429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 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: 0.692 AC: 105181 AN: 152008 Hom.: 37371 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.692 AC: 105295 AN: 152126 Hom.: 37429 Cov.: 32 AF XY: 0.689 AC XY: 51233 AN XY: 74370

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.688

Alfa AF: 0.707 Hom.: 5517

Bravo AF: 0.685

Asia WGS AF: 0.592 AC: 2055 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6972429; hg19: chr7-41894842;