rs2486064

Positions:

• chr1-203199636-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.688

Alfa AF: 0.608 Hom.: 40718

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2486064; hg19: chr1-203168764;