rs11955354

Variant names:

• chr5-40457357-G-A
• rs11955354

Your query was ambiguous. Multiple possible variants found:

• chr5-40457357-G-A
• chr5-40457357-G-C

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 0.385 in 151,892 control chromosomes in the GnomAD database, including 11,861 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 0.39 (11861 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.385 AC: 58463 AN: 151774 Hom.: 11860 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.385 AC: 58487 AN: 151892 Hom.: 11861 Cov.: 31 AF XY: 0.393 AC XY: 29178 AN XY: 74220

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.372

Alfa AF: 0.345 Hom.: 3233

Bravo AF: 0.383

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11955354; hg19: chr5-40457459;