rs1420960

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.598

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1420960; hg19: chr18-25198599;