chr18-60061837-C-T

Variant names:

• chr18-60061837-C-T
• rs3897644

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 0.488 in 151,896 control chromosomes in the GnomAD database, including 19,836 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 0.49 (19836 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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: 0.488 AC: 74131 AN: 151778 Hom.: 19834 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.488 AC: 74162 AN: 151896 Hom.: 19836 Cov.: 31 AF XY: 0.492 AC XY: 36511 AN XY: 74202

African (AFR) AF: 0.273 AC: 11307 AN: 41416

American (AMR) AF: 0.621 AC: 9478 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2090 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4182 AN: 5174

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4816

European-Finnish (FIN) AF: 0.554 AC: 5817 AN: 10508

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37286 AN: 67930

Other (OTH) AF: 0.512 AC: 1078 AN: 2106

Alfa AF: 0.534 Hom.: 13886

Bravo AF: 0.488

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.65
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs3897644; hg19: chr18-57729069;