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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.392 AC: 16233 AN: 41368

American (AMR) AF: 0.412 AC: 6289 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3902 AN: 5158

South Asian (SAS) AF: 0.521 AC: 2513 AN: 4820

European-Finnish (FIN) AF: 0.427 AC: 4495 AN: 10528

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22726 AN: 67972

Other (OTH) AF: 0.372 AC: 783 AN: 2104

Alfa AF: 0.349 Hom.: 5325

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
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs11955354; hg19: chr5-40457459;