18-69349243-T-C

Variant names:

• chr18-69349243-T-C
• rs17080877

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 0.157 in 152,072 control chromosomes in the GnomAD database, including 1,980 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 0.16 (1980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.157 AC: 23884 AN: 151954 Hom.: 1978 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.157 AC: 23912 AN: 152072 Hom.: 1980 Cov.: 32 AF XY: 0.155 AC XY: 11504 AN XY: 74328

African (AFR) AF: 0.176 AC: 7309 AN: 41484

American (AMR) AF: 0.180 AC: 2746 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1296 AN: 5174

South Asian (SAS) AF: 0.118 AC: 566 AN: 4816

European-Finnish (FIN) AF: 0.0892 AC: 945 AN: 10600

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9687 AN: 67960

Other (OTH) AF: 0.193 AC: 408 AN: 2116

Alfa AF: 0.152 Hom.: 3035

Bravo AF: 0.170

Asia WGS AF: 0.185 AC: 641 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.6
DANN	Benign	0.93
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs17080877; hg19: chr18-67016479;