rs2006747

Variant names:

• chr18-50441988-G-C
• rs2006747

Your query was ambiguous. Multiple possible variants found:

• chr18-50441988-G-C
• chr18-50441988-G-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 0.442 in 152,054 control chromosomes in the GnomAD database, including 15,394 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 0.44 (15394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.442 AC: 67093 AN: 151934 Hom.: 15365 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.442 AC: 67180 AN: 152054 Hom.: 15394 Cov.: 32 AF XY: 0.440 AC XY: 32703 AN XY: 74312

African (AFR) AF: 0.565 AC: 23451 AN: 41478

American (AMR) AF: 0.396 AC: 6052 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3466

East Asian (EAS) AF: 0.447 AC: 2307 AN: 5166

South Asian (SAS) AF: 0.420 AC: 2024 AN: 4824

European-Finnish (FIN) AF: 0.352 AC: 3720 AN: 10558

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

European-Non Finnish (NFE) AF: 0.390 AC: 26506 AN: 67984

Other (OTH) AF: 0.445 AC: 939 AN: 2110

Alfa AF: 0.257 Hom.: 571

Bravo AF: 0.448

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2006747; hg19: chr18-47968358;