rs6745660

Variant names:

• chr2-197484812-A-G
• rs6745660

Your query was ambiguous. Multiple possible variants found:

• chr2-197484812-A-G
• chr2-197484812-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 0.432 in 151,882 control chromosomes in the GnomAD database, including 14,620 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 0.43 (14620 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65660 AN: 151766 Hom.: 14629 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.432 AC: 65653 AN: 151882 Hom.: 14620 Cov.: 31 AF XY: 0.430 AC XY: 31927 AN XY: 74212

African (AFR) AF: 0.365 AC: 15123 AN: 41408

American (AMR) AF: 0.411 AC: 6264 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1755 AN: 3464

East Asian (EAS) AF: 0.264 AC: 1366 AN: 5176

South Asian (SAS) AF: 0.563 AC: 2714 AN: 4820

European-Finnish (FIN) AF: 0.384 AC: 4041 AN: 10516

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32825 AN: 67940

Other (OTH) AF: 0.445 AC: 938 AN: 2110

Alfa AF: 0.467 Hom.: 44087

Bravo AF: 0.425

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.86
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6745660; hg19: chr2-198349536;