1-237940201-C-T

Variant names:

• chr1-237940201-C-T
• rs2499604

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 0.534 in 151,860 control chromosomes in the GnomAD database, including 22,473 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 0.53 (22473 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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: 0.533 AC: 80947 AN: 151742 Hom.: 22436 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.534 AC: 81029 AN: 151860 Hom.: 22473 Cov.: 31 AF XY: 0.540 AC XY: 40042 AN XY: 74214

African (AFR) AF: 0.700 AC: 28996 AN: 41416

American (AMR) AF: 0.482 AC: 7351 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2663 AN: 5142

South Asian (SAS) AF: 0.547 AC: 2635 AN: 4814

European-Finnish (FIN) AF: 0.530 AC: 5579 AN: 10528

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30706 AN: 67912

Other (OTH) AF: 0.502 AC: 1060 AN: 2112

Alfa AF: 0.470 Hom.: 79945

Bravo AF: 0.532

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.74
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2499604; hg19: chr1-238103501;