rs31210

Variant names:

• chr5-135025330-G-A
• rs31210

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 0.231 in 152,104 control chromosomes in the GnomAD database, including 4,440 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 0.23 (4440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 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: 0.231 AC: 35067 AN: 151986 Hom.: 4444 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.231 AC: 35072 AN: 152104 Hom.: 4440 Cov.: 32 AF XY: 0.233 AC XY: 17312 AN XY: 74346

African (AFR) AF: 0.142 AC: 5906 AN: 41528

American (AMR) AF: 0.259 AC: 3956 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1658 AN: 5154

South Asian (SAS) AF: 0.377 AC: 1811 AN: 4808

European-Finnish (FIN) AF: 0.243 AC: 2571 AN: 10584

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17474 AN: 67970

Other (OTH) AF: 0.227 AC: 480 AN: 2112

Alfa AF: 0.248 Hom.: 14179

Bravo AF: 0.224

Asia WGS AF: 0.389 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.66
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs31210; hg19: chr5-134361020; COSMIC: COSV54761704;