rs7124676

Positions:

• chr11-64545819-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;