rs6972429

Positions:

• chr7-41855244-C-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 0.692 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;