rs17385253

Variant names:

• chr1-34429408-T-C
• rs17385253

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 0.196 in 152,144 control chromosomes in the GnomAD database, including 3,570 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 0.20 (3570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29763 AN: 152026 Hom.: 3567 Cov.: 32

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.196 AC: 29766 AN: 152144 Hom.: 3570 Cov.: 32 AF XY: 0.199 AC XY: 14804 AN XY: 74370

African (AFR) AF: 0.0734 AC: 3048 AN: 41546

American (AMR) AF: 0.169 AC: 2578 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1206 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1567 AN: 5166

South Asian (SAS) AF: 0.157 AC: 758 AN: 4822

European-Finnish (FIN) AF: 0.340 AC: 3591 AN: 10554

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16316 AN: 67970

Other (OTH) AF: 0.200 AC: 423 AN: 2110

Alfa AF: 0.228 Hom.: 16245

Bravo AF: 0.179

Asia WGS AF: 0.191 AC: 664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.032
DANN	Benign	0.44
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs17385253; hg19: chr1-34895009;