rs251398

Variant names:

• chr5-68213973-T-C
• rs251398

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 0.497 in 152,118 control chromosomes in the GnomAD database, including 19,618 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 0.50 (19618 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 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: 0.497 AC: 75503 AN: 151998 Hom.: 19566 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.497 AC: 75614 AN: 152118 Hom.: 19618 Cov.: 33 AF XY: 0.496 AC XY: 36878 AN XY: 74360

African (AFR) AF: 0.634 AC: 26294 AN: 41472

American (AMR) AF: 0.481 AC: 7353 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3470

East Asian (EAS) AF: 0.727 AC: 3766 AN: 5182

South Asian (SAS) AF: 0.449 AC: 2163 AN: 4822

European-Finnish (FIN) AF: 0.402 AC: 4250 AN: 10566

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29324 AN: 68004

Other (OTH) AF: 0.443 AC: 937 AN: 2116

Alfa AF: 0.469 Hom.: 7255

Bravo AF: 0.512

Asia WGS AF: 0.590 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.27
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs251398; hg19: chr5-67509801; COSMIC: COSV72884230;