18-78595084-C-T

Variant names:

• chr18-78595084-C-T
• rs7231100

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 0.214 in 152,084 control chromosomes in the GnomAD database, including 4,275 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 0.21 (4275 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 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: 0.214 AC: 32462 AN: 151966 Hom.: 4267 Cov.: 33

Gnomad AFR AF: 0.0679

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.214 AC: 32486 AN: 152084 Hom.: 4275 Cov.: 33 AF XY: 0.215 AC XY: 15999 AN XY: 74336

African (AFR) AF: 0.0679 AC: 2817 AN: 41514

American (AMR) AF: 0.244 AC: 3736 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3468

East Asian (EAS) AF: 0.141 AC: 729 AN: 5162

South Asian (SAS) AF: 0.254 AC: 1223 AN: 4816

European-Finnish (FIN) AF: 0.308 AC: 3255 AN: 10558

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19310 AN: 67954

Other (OTH) AF: 0.226 AC: 478 AN: 2114

Alfa AF: 0.224 Hom.: 1095

Bravo AF: 0.203

Asia WGS AF: 0.183 AC: 641 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7231100; hg19: chr18-76355084;