rs2486064

Variant names:

• chr1-203199636-T-C
• rs2486064

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 0.69 in 151,996 control chromosomes in the GnomAD database, including 38,068 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 0.69 (38068 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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: 0.690 AC: 104831 AN: 151878 Hom.: 38006 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.690 AC: 104951 AN: 151996 Hom.: 38068 Cov.: 31 AF XY: 0.688 AC XY: 51123 AN XY: 74280

African (AFR) AF: 0.918 AC: 38068 AN: 41490

American (AMR) AF: 0.749 AC: 11438 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2304 AN: 3470

East Asian (EAS) AF: 0.622 AC: 3206 AN: 5156

South Asian (SAS) AF: 0.600 AC: 2885 AN: 4808

European-Finnish (FIN) AF: 0.509 AC: 5383 AN: 10570

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39354 AN: 67912

Other (OTH) AF: 0.688 AC: 1452 AN: 2112

Alfa AF: 0.617 Hom.: 58071

Bravo AF: 0.723

Asia WGS AF: 0.644 AC: 2238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.031
DANN	Benign	0.41
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2486064; hg19: chr1-203168764;