rs17385253

Variant names:

• chr1-34429408-T-C
• rs17385253

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 0.196 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

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 (EAS) allele frequency at 95% confidence interval = 0.291 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: 0.196 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

Gnomad4 AFR AF: 0.0734

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.200

Alfa AF: 0.234 Hom.: 7320

Bravo AF: 0.179

Asia WGS AF: 0.191 AC: 664 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	0.032
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17385253; hg19: chr1-34895009;