chr18-60169647-T-C

Variant names:

• chr18-60169647-T-C
• rs2051311

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.51 in 152,072 control chromosomes in the GnomAD database, including 21,801 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 0.51 (21801 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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: 0.510 AC: 77450 AN: 151954 Hom.: 21767 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.510 AC: 77533 AN: 152072 Hom.: 21801 Cov.: 32 AF XY: 0.504 AC XY: 37481 AN XY: 74364

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.466

Alfa AF: 0.439 Hom.: 17111

Bravo AF: 0.513

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2051311; hg19: chr18-57836880;