rs1908490

Variant names:

• chr1-4252145-C-T
• rs1908490

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 0.402 in 152,008 control chromosomes in the GnomAD database, including 14,109 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 0.40 (14109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 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: 0.402 AC: 61062 AN: 151890 Hom.: 14102 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.402 AC: 61095 AN: 152008 Hom.: 14109 Cov.: 32 AF XY: 0.403 AC XY: 29973 AN XY: 74286

African (AFR) AF: 0.167 AC: 6933 AN: 41486

American (AMR) AF: 0.513 AC: 7842 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1573 AN: 3464

East Asian (EAS) AF: 0.226 AC: 1165 AN: 5160

South Asian (SAS) AF: 0.505 AC: 2428 AN: 4810

European-Finnish (FIN) AF: 0.497 AC: 5247 AN: 10558

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34529 AN: 67940

Other (OTH) AF: 0.399 AC: 845 AN: 2116

Alfa AF: 0.471 Hom.: 29742

Bravo AF: 0.388

Asia WGS AF: 0.412 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.83
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1908490; hg19: chr1-4312205; COSMIC: COSV53274065;