rs2495408

Variant names:

• chr1-187827875-C-T
• rs2495408

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 0.442 in 152,108 control chromosomes in the GnomAD database, including 15,335 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 0.44 (15335 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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: 0.442 AC: 67161 AN: 151990 Hom.: 15328 Cov.: 34

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.442 AC: 67182 AN: 152108 Hom.: 15335 Cov.: 34 AF XY: 0.442 AC XY: 32858 AN XY: 74358

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.443

Alfa AF: 0.457 Hom.: 2776

Bravo AF: 0.431

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2495408; hg19: chr1-187797006;