7-64272953-A-G

Position:

• chr7-64272953-A-G

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 0.59 in 152,018 control chromosomes in the GnomAD database, including 27,925 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 0.59 (27925 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 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: 0.590 AC: 89685 AN: 151900 Hom.: 27918 Cov.: 34

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.590 AC: 89715 AN: 152018 Hom.: 27925 Cov.: 34 AF XY: 0.594 AC XY: 44136 AN XY: 74282

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.630

Alfa AF: 0.650 Hom.: 12862

Bravo AF: 0.578

Asia WGS AF: 0.697 AC: 2421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10266483; hg19: chr7-63733331;