chr18-67410688-T-C

Variant names:

• chr18-67410688-T-C
• rs10871618

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 0.139 in 152,136 control chromosomes in the GnomAD database, including 1,515 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 0.14 (1515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21133 AN: 152022 Hom.: 1515 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.139 AC: 21141 AN: 152136 Hom.: 1515 Cov.: 32 AF XY: 0.140 AC XY: 10384 AN XY: 74360

African (AFR) AF: 0.150 AC: 6228 AN: 41510

American (AMR) AF: 0.154 AC: 2358 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.145 AC: 752 AN: 5182

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4830

European-Finnish (FIN) AF: 0.116 AC: 1231 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8627 AN: 67970

Other (OTH) AF: 0.144 AC: 303 AN: 2110

Alfa AF: 0.132 Hom.: 1743

Bravo AF: 0.142

Asia WGS AF: 0.180 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.78
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10871618; hg19: chr18-65077925;