rs1317170

Positions:

• chr1-226410613-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;