rs11954565

Variant names:

• chr5-175422904-A-G
• rs11954565

Your query was ambiguous. Multiple possible variants found:

• chr5-175422904-A-G
• chr5-175422904-A-T

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 0.392 in 152,042 control chromosomes in the GnomAD database, including 11,931 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 (11931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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: 0.392 AC: 59483 AN: 151924 Hom.: 11923 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.392 AC: 59532 AN: 152042 Hom.: 11931 Cov.: 32 AF XY: 0.391 AC XY: 29068 AN XY: 74320

African (AFR) AF: 0.434 AC: 18009 AN: 41474

American (AMR) AF: 0.459 AC: 7001 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3468

East Asian (EAS) AF: 0.540 AC: 2790 AN: 5162

South Asian (SAS) AF: 0.291 AC: 1400 AN: 4814

European-Finnish (FIN) AF: 0.338 AC: 3579 AN: 10582

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24164 AN: 67958

Other (OTH) AF: 0.411 AC: 867 AN: 2110

Alfa AF: 0.366 Hom.: 14672

Bravo AF: 0.402

Asia WGS AF: 0.426 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.80
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs11954565; hg19: chr5-174849907; COSMIC: COSV107163931;