rs2342510

Variant names:

• chr4-59838661-C-T
• rs2342510

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 0.503 in 151,682 control chromosomes in the GnomAD database, including 19,500 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 (19500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.583 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: 0.503 AC: 76240 AN: 151566 Hom.: 19490 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.503 AC: 76261 AN: 151682 Hom.: 19500 Cov.: 32 AF XY: 0.499 AC XY: 37010 AN XY: 74108

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.489

Alfa AF: 0.513 Hom.: 2923

Bravo AF: 0.513

Asia WGS AF: 0.282 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.78
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2342510; hg19: chr4-60704379;