chr18-53861827-T-A

Variant names:

• chr18-53861827-T-A
• rs1646807

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 0.78 in 152,062 control chromosomes in the GnomAD database, including 46,783 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 0.78 (46783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.780 AC: 118486 AN: 151944 Hom.: 46745 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.780 AC: 118581 AN: 152062 Hom.: 46783 Cov.: 31 AF XY: 0.783 AC XY: 58186 AN XY: 74344

African (AFR) AF: 0.662 AC: 27411 AN: 41416

American (AMR) AF: 0.864 AC: 13221 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2901 AN: 3472

East Asian (EAS) AF: 0.894 AC: 4618 AN: 5164

South Asian (SAS) AF: 0.874 AC: 4211 AN: 4816

European-Finnish (FIN) AF: 0.783 AC: 8283 AN: 10580

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55476 AN: 67992

Other (OTH) AF: 0.818 AC: 1731 AN: 2116

Alfa AF: 0.799 Hom.: 6060

Bravo AF: 0.779

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.53
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1646807; hg19: chr18-51388197;