rs6747918

Variant names:

• chr2-201232852-G-A
• rs6747918

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 0.541 in 151,994 control chromosomes in the GnomAD database, including 23,144 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 0.54 (23144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82102 AN: 151876 Hom.: 23102 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.541 AC: 82200 AN: 151994 Hom.: 23144 Cov.: 32 AF XY: 0.532 AC XY: 39531 AN XY: 74294

African (AFR) AF: 0.679 AC: 28152 AN: 41432

American (AMR) AF: 0.445 AC: 6801 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1839 AN: 3468

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5182

South Asian (SAS) AF: 0.319 AC: 1539 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5438 AN: 10538

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35666 AN: 67970

Other (OTH) AF: 0.526 AC: 1109 AN: 2108

Alfa AF: 0.522 Hom.: 10749

Bravo AF: 0.541

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6747918; hg19: chr2-202097575;