rs1460465

Variant names:

• chr13-71889403-G-A
• rs1460465

Your query was ambiguous. Multiple possible variants found:

• chr13-71889403-G-A
• chr13-71889403-G-T

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 0.84 in 152,096 control chromosomes in the GnomAD database, including 56,942 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 0.84 (56942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127638 AN: 151976 Hom.: 56935 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.840 AC: 127693 AN: 152096 Hom.: 56942 Cov.: 32 AF XY: 0.840 AC XY: 62438 AN XY: 74360

African (AFR) AF: 0.542 AC: 22449 AN: 41404

American (AMR) AF: 0.883 AC: 13500 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3421 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2603 AN: 5146

South Asian (SAS) AF: 0.939 AC: 4524 AN: 4818

European-Finnish (FIN) AF: 0.980 AC: 10408 AN: 10622

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67749 AN: 68030

Other (OTH) AF: 0.872 AC: 1841 AN: 2112

Alfa AF: 0.932 Hom.: 24305

Bravo AF: 0.817

Asia WGS AF: 0.756 AC: 2621 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.69
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1460465; hg19: chr13-72463541;