chr7-64272953-A-G

Variant names:

• chr7-64272953-A-G
• rs10266483

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.382 AC: 15838 AN: 41426

American (AMR) AF: 0.652 AC: 9958 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2009 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4306 AN: 5174

South Asian (SAS) AF: 0.668 AC: 3223 AN: 4822

European-Finnish (FIN) AF: 0.687 AC: 7252 AN: 10556

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45144 AN: 67972

Other (OTH) AF: 0.630 AC: 1332 AN: 2114

Alfa AF: 0.656 Hom.: 27522

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
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs10266483; hg19: chr7-63733331;