rs1317170

Variant names:

• chr1-226410613-T-C
• rs1317170

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 0.225 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
• Publications: 7 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 = 0.432 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.269 AC: 10956 AN: 40782

American (AMR) AF: 0.320 AC: 4818 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3460

East Asian (EAS) AF: 0.448 AC: 2225 AN: 4968

South Asian (SAS) AF: 0.195 AC: 925 AN: 4748

European-Finnish (FIN) AF: 0.256 AC: 2619 AN: 10234

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11115 AN: 67770

Other (OTH) AF: 0.209 AC: 437 AN: 2094

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1317170; hg19: chr1-226598314;