rs254893

Variant names:

• chr5-171649223-G-A
• rs254893

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 0.209 in 151,916 control chromosomes in the GnomAD database, including 3,682 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 0.21 (3682 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 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: 0.209 AC: 31726 AN: 151796 Hom.: 3681 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.209 AC: 31725 AN: 151916 Hom.: 3682 Cov.: 31 AF XY: 0.209 AC XY: 15494 AN XY: 74232

African (AFR) AF: 0.114 AC: 4708 AN: 41476

American (AMR) AF: 0.262 AC: 4003 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3468

East Asian (EAS) AF: 0.113 AC: 582 AN: 5144

South Asian (SAS) AF: 0.221 AC: 1059 AN: 4802

European-Finnish (FIN) AF: 0.250 AC: 2629 AN: 10530

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17272 AN: 67912

Other (OTH) AF: 0.207 AC: 437 AN: 2110

Alfa AF: 0.232 Hom.: 10354

Bravo AF: 0.203

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.81
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs254893; hg19: chr5-171076227; COSMIC: COSV60230939;