chr1-187827875-C-T

Variant names:

• chr1-187827875-C-T
• rs2495408

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 0.442 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.331 AC: 13718 AN: 41500

American (AMR) AF: 0.413 AC: 6309 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2454 AN: 5172

South Asian (SAS) AF: 0.446 AC: 2150 AN: 4822

European-Finnish (FIN) AF: 0.543 AC: 5735 AN: 10568

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33861 AN: 67982

Other (OTH) AF: 0.443 AC: 935 AN: 2112

Alfa AF: 0.454 Hom.: 2819

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
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs2495408; hg19: chr1-187797006;