1-147539962-C-T

Variant names:

• chr1-147539962-C-T
• rs3806218

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 0.477 in 151,982 control chromosomes in the GnomAD database, including 20,615 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 0.48 (20615 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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: 0.477 AC: 72466 AN: 151864 Hom.: 20565 Cov.: 31

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.477 AC: 72558 AN: 151982 Hom.: 20615 Cov.: 31 AF XY: 0.469 AC XY: 34850 AN XY: 74282

African (AFR) AF: 0.808 AC: 33497 AN: 41452

American (AMR) AF: 0.371 AC: 5663 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1587 AN: 5146

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4824

European-Finnish (FIN) AF: 0.329 AC: 3474 AN: 10566

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24588 AN: 67944

Other (OTH) AF: 0.442 AC: 932 AN: 2108

Alfa AF: 0.399 Hom.: 17632

Bravo AF: 0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3806218; hg19: chr1-147011783;