rs257314

Variant names:

• chr5-103085391-T-C
• rs257314

Your query was ambiguous. Multiple possible variants found:

• chr5-103085391-T-C
• chr5-103085391-T-G

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 0.257 in 152,092 control chromosomes in the GnomAD database, including 5,574 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 0.26 (5574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.257 AC: 39114 AN: 151974 Hom.: 5573 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.257 AC: 39146 AN: 152092 Hom.: 5574 Cov.: 32 AF XY: 0.256 AC XY: 19041 AN XY: 74360

African (AFR) AF: 0.146 AC: 6075 AN: 41506

American (AMR) AF: 0.236 AC: 3604 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2315 AN: 5150

South Asian (SAS) AF: 0.145 AC: 699 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3381 AN: 10550

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21295 AN: 67998

Other (OTH) AF: 0.253 AC: 533 AN: 2108

Alfa AF: 0.269 Hom.: 761

Bravo AF: 0.248

Asia WGS AF: 0.264 AC: 917 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.69
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs257314; hg19: chr5-102421095; COSMIC: COSV67536311;