1-206955921-C-T

Variant names:

• chr1-206955921-C-T
• rs10863962

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 0.358 in 152,034 control chromosomes in the GnomAD database, including 11,714 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 0.36 (11714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 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: 0.357 AC: 54306 AN: 151916 Hom.: 11696 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.358 AC: 54367 AN: 152034 Hom.: 11714 Cov.: 32 AF XY: 0.350 AC XY: 25987 AN XY: 74312

African (AFR) AF: 0.600 AC: 24876 AN: 41442

American (AMR) AF: 0.365 AC: 5576 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3470

East Asian (EAS) AF: 0.0647 AC: 335 AN: 5174

South Asian (SAS) AF: 0.159 AC: 764 AN: 4812

European-Finnish (FIN) AF: 0.184 AC: 1947 AN: 10572

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18255 AN: 67980

Other (OTH) AF: 0.378 AC: 800 AN: 2114

Alfa AF: 0.238 Hom.: 840

Bravo AF: 0.382

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.36
DANN	Benign	0.33
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs10863962; hg19: chr1-207129266;