rs1395558

Variant names:

• chr11-6706237-A-G
• rs1395558

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 0.556 in 152,070 control chromosomes in the GnomAD database, including 24,752 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 0.56 (24752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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 = 0.654 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: 0.556 AC: 84490 AN: 151952 Hom.: 24747 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.556 AC: 84519 AN: 152070 Hom.: 24752 Cov.: 32 AF XY: 0.554 AC XY: 41165 AN XY: 74304

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.584

Alfa AF: 0.641 Hom.: 71047

Bravo AF: 0.533

Asia WGS AF: 0.467 AC: 1625 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	0.13
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395558; hg19: chr11-6727468;