1-4636032-C-T

Variant names:

• chr1-4636032-C-T
• rs2071967

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 0.224 in 152,134 control chromosomes in the GnomAD database, including 4,469 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 0.22 (4469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 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: 0.224 AC: 34056 AN: 152016 Hom.: 4472 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.224 AC: 34059 AN: 152134 Hom.: 4469 Cov.: 32 AF XY: 0.232 AC XY: 17221 AN XY: 74354

African (AFR) AF: 0.135 AC: 5587 AN: 41516

American (AMR) AF: 0.231 AC: 3528 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2930 AN: 5174

South Asian (SAS) AF: 0.449 AC: 2165 AN: 4822

European-Finnish (FIN) AF: 0.205 AC: 2161 AN: 10566

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

European-Non Finnish (NFE) AF: 0.234 AC: 15934 AN: 67976

Other (OTH) AF: 0.232 AC: 491 AN: 2116

Alfa AF: 0.240 Hom.: 4002

Bravo AF: 0.217

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2071967; hg19: chr1-4696092;