chr11-64545819-G-A

Variant names:

• chr11-64545819-G-A
• rs7124676

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 0.373 in 152,186 control chromosomes in the GnomAD database, including 13,548 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 0.37 (13548 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 14 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 = 0.541 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: 0.373 AC: 56719 AN: 152068 Hom.: 13552 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.373 AC: 56715 AN: 152186 Hom.: 13548 Cov.: 33 AF XY: 0.366 AC XY: 27256 AN XY: 74398

African (AFR) AF: 0.115 AC: 4779 AN: 41542

American (AMR) AF: 0.321 AC: 4907 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5188

South Asian (SAS) AF: 0.375 AC: 1813 AN: 4832

European-Finnish (FIN) AF: 0.443 AC: 4687 AN: 10574

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37079 AN: 67960

Other (OTH) AF: 0.377 AC: 798 AN: 2116

Alfa AF: 0.426 Hom.: 19029

Bravo AF: 0.351

Asia WGS AF: 0.170 AC: 594 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	0.67
DANN	Benign	0.58
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7124676; hg19: chr11-64313291;