rs7124355

Variant names:

• chr11-17391413-A-G
• rs7124355

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 0.739 in 152,094 control chromosomes in the GnomAD database, including 42,643 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 0.74 (42643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 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: 0.739 AC: 112247 AN: 151976 Hom.: 42592 Cov.: 32

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.739 AC: 112358 AN: 152094 Hom.: 42643 Cov.: 32 AF XY: 0.732 AC XY: 54422 AN XY: 74326

African (AFR) AF: 0.932 AC: 38691 AN: 41536

American (AMR) AF: 0.701 AC: 10722 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2433 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3319 AN: 5134

South Asian (SAS) AF: 0.633 AC: 3049 AN: 4814

European-Finnish (FIN) AF: 0.565 AC: 5967 AN: 10564

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45976 AN: 67968

Other (OTH) AF: 0.733 AC: 1546 AN: 2108

Alfa AF: 0.710 Hom.: 54231

Bravo AF: 0.753

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.45
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs7124355; hg19: chr11-17412960;