chr1-62339468-G-C

Variant names:

• chr1-62339468-G-C
• rs2182241

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 0.461 in 151,888 control chromosomes in the GnomAD database, including 16,292 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 0.46 (16292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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: 0.460 AC: 69885 AN: 151770 Hom.: 16274 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.461 AC: 69949 AN: 151888 Hom.: 16292 Cov.: 31 AF XY: 0.459 AC XY: 34097 AN XY: 74218

African (AFR) AF: 0.500 AC: 20692 AN: 41404

American (AMR) AF: 0.467 AC: 7138 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1555 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2729 AN: 5140

South Asian (SAS) AF: 0.422 AC: 2027 AN: 4798

European-Finnish (FIN) AF: 0.444 AC: 4683 AN: 10552

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29624 AN: 67928

Other (OTH) AF: 0.452 AC: 955 AN: 2112

Alfa AF: 0.451 Hom.: 2187

Bravo AF: 0.466

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2182241; hg19: chr1-62805139;