18-64751208-A-C

Variant names:

• chr18-64751208-A-C
• rs17073641

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 0.411 in 151,624 control chromosomes in the GnomAD database, including 13,084 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 0.41 (13084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 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: 0.411 AC: 62300 AN: 151506 Hom.: 13084 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.411 AC: 62320 AN: 151624 Hom.: 13084 Cov.: 32 AF XY: 0.418 AC XY: 30927 AN XY: 74058

African (AFR) AF: 0.326 AC: 13490 AN: 41354

American (AMR) AF: 0.386 AC: 5853 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3468

East Asian (EAS) AF: 0.398 AC: 2044 AN: 5132

South Asian (SAS) AF: 0.501 AC: 2400 AN: 4786

European-Finnish (FIN) AF: 0.502 AC: 5274 AN: 10508

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29897 AN: 67888

Other (OTH) AF: 0.420 AC: 886 AN: 2112

Alfa AF: 0.417 Hom.: 26663

Bravo AF: 0.394

Asia WGS AF: 0.431 AC: 1499 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.32
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs17073641; hg19: chr18-62418444;