rs1317170

Variant names:

• chr1-226410613-T-C
• rs1317170

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 0.225 in 150,328 control chromosomes in the GnomAD database, including 4,372 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 0.22 (4372 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

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 = 0.432 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: 0.224 AC: 33698 AN: 150212 Hom.: 4352 Cov.: 28

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.225 AC: 33770 AN: 150328 Hom.: 4372 Cov.: 28 AF XY: 0.229 AC XY: 16802 AN XY: 73322

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.209

Alfa AF: 0.203 Hom.: 457

Bravo AF: 0.236

Asia WGS AF: 0.302 AC: 1049 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	2.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317170; hg19: chr1-226598314;