rs7124676

Variant names:

• chr11-64545819-G-A
• rs7124676

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 0.373 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.377

Alfa AF: 0.484 Hom.: 13146

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7124676; hg19: chr11-64313291;