rs1420960

Variant names:

• chr18-27618635-T-A
• rs1420960

Your query was ambiguous. Multiple possible variants found:

• chr18-27618635-T-A
• chr18-27618635-T-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.593 in 152,014 control chromosomes in the GnomAD database, including 27,071 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 0.59 (27071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.647 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: 0.593 AC: 90020 AN: 151896 Hom.: 27037 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.593 AC: 90114 AN: 152014 Hom.: 27071 Cov.: 32 AF XY: 0.592 AC XY: 43991 AN XY: 74288

African (AFR) AF: 0.652 AC: 27051 AN: 41484

American (AMR) AF: 0.658 AC: 10058 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3351 AN: 5148

South Asian (SAS) AF: 0.568 AC: 2732 AN: 4808

European-Finnish (FIN) AF: 0.531 AC: 5605 AN: 10560

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37204 AN: 67938

Other (OTH) AF: 0.598 AC: 1266 AN: 2116

Alfa AF: 0.590 Hom.: 3315

Bravo AF: 0.609

Asia WGS AF: 0.614 AC: 2136 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	17
DANN	Benign	0.80
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1420960; hg19: chr18-25198599;