18-55195877-C-G

Variant names:

• chr18-55195877-C-G
• rs1970671

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 0.268 in 149,262 control chromosomes in the GnomAD database, including 5,830 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 0.27 (5830 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 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: 0.268 AC: 39980 AN: 149214 Hom.: 5833 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.268 AC: 39992 AN: 149262 Hom.: 5830 Cov.: 31 AF XY: 0.272 AC XY: 19771 AN XY: 72580

African (AFR) AF: 0.134 AC: 5432 AN: 40510

American (AMR) AF: 0.278 AC: 4163 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3462

East Asian (EAS) AF: 0.502 AC: 2569 AN: 5120

South Asian (SAS) AF: 0.418 AC: 1970 AN: 4712

European-Finnish (FIN) AF: 0.321 AC: 3106 AN: 9688

Middle Eastern (MID) AF: 0.387 AC: 109 AN: 282

European-Non Finnish (NFE) AF: 0.305 AC: 20595 AN: 67526

Other (OTH) AF: 0.283 AC: 584 AN: 2060

Alfa AF: 0.283 Hom.: 3416

Bravo AF: 0.257

Asia WGS AF: 0.400 AC: 1389 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.56
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1970671; hg19: chr18-52863108;