rs675566

Variant names:

• chr18-40999812-A-C
• rs675566

Your query was ambiguous. Multiple possible variants found:

• chr18-40999812-A-C
• chr18-40999812-A-T

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 0.236 in 151,798 control chromosomes in the GnomAD database, including 5,151 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 0.24 (5151 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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: 0.236 AC: 35808 AN: 151680 Hom.: 5154 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.236 AC: 35803 AN: 151798 Hom.: 5151 Cov.: 32 AF XY: 0.236 AC XY: 17546 AN XY: 74194

African (AFR) AF: 0.102 AC: 4227 AN: 41520

American (AMR) AF: 0.208 AC: 3170 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3468

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5188

South Asian (SAS) AF: 0.204 AC: 983 AN: 4822

European-Finnish (FIN) AF: 0.350 AC: 3690 AN: 10536

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21806 AN: 67718

Other (OTH) AF: 0.247 AC: 519 AN: 2104

Alfa AF: 0.281 Hom.: 13133

Bravo AF: 0.222

Asia WGS AF: 0.0990 AC: 342 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.31
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs675566; hg19: chr18-38579776;