chr18-75815872-T-C

Variant names:

• chr18-75815872-T-C
• rs3943367

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 0.0526 in 152,238 control chromosomes in the GnomAD database, including 504 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 0.053 (504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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: 0.0525 AC: 7985 AN: 152120 Hom.: 504 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00792

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0526 AC: 8003 AN: 152238 Hom.: 504 Cov.: 32 AF XY: 0.0521 AC XY: 3875 AN XY: 74434

African (AFR) AF: 0.152 AC: 6310 AN: 41516

American (AMR) AF: 0.0275 AC: 421 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3468

East Asian (EAS) AF: 0.0659 AC: 341 AN: 5176

South Asian (SAS) AF: 0.00725 AC: 35 AN: 4826

European-Finnish (FIN) AF: 0.0197 AC: 209 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00792 AC: 539 AN: 68018

Other (OTH) AF: 0.0412 AC: 87 AN: 2114

Alfa AF: 0.0240 Hom.: 238

Bravo AF: 0.0576

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs3943367; hg19: chr18-73527827;