rs251398

Variant names:

• chr5-68213973-T-C
• rs251398

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 0.497 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.443

Alfa AF: 0.467 Hom.: 5799

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

Splicing

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

Publications

LitVar

Other links and lift over

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