1-205912066-T-C

Variant names:

• chr1-205912066-T-C
• rs17433088

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 0.244 in 152,074 control chromosomes in the GnomAD database, including 4,673 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 0.24 (4673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 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: 0.243 AC: 36989 AN: 151954 Hom.: 4658 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.244 AC: 37032 AN: 152074 Hom.: 4673 Cov.: 32 AF XY: 0.248 AC XY: 18407 AN XY: 74318

African (AFR) AF: 0.198 AC: 8204 AN: 41460

American (AMR) AF: 0.272 AC: 4151 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1330 AN: 5180

South Asian (SAS) AF: 0.375 AC: 1803 AN: 4812

European-Finnish (FIN) AF: 0.253 AC: 2684 AN: 10588

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17190 AN: 67970

Other (OTH) AF: 0.246 AC: 519 AN: 2110

Alfa AF: 0.250 Hom.: 10476

Bravo AF: 0.237

Asia WGS AF: 0.347 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.80
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs17433088; hg19: chr1-205881194;