chr7-64042251-T-G

Variant names:

• chr7-64042251-T-G
• rs11520658

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 0.0402 in 152,248 control chromosomes in the GnomAD database, including 167 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 0.040 (167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0604 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: 0.0403 AC: 6130 AN: 152130 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0402 AC: 6127 AN: 152248 Hom.: 167 Cov.: 32 AF XY: 0.0371 AC XY: 2765 AN XY: 74448

African (AFR) AF: 0.0113 AC: 471 AN: 41538

American (AMR) AF: 0.0344 AC: 527 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3466

East Asian (EAS) AF: 0.000582 AC: 3 AN: 5154

South Asian (SAS) AF: 0.0186 AC: 90 AN: 4828

European-Finnish (FIN) AF: 0.0171 AC: 182 AN: 10626

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0619 AC: 4213 AN: 68016

Other (OTH) AF: 0.0587 AC: 124 AN: 2114

Alfa AF: 0.0601 Hom.: 599

Bravo AF: 0.0416

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.36
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs11520658; hg19: chr7-63502629;