rs6745660

Positions:

• chr2-197484812-A-G
• chr2-197484812-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.445

Alfa AF: 0.476 Hom.: 27529

Bravo AF: 0.425

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6745660; hg19: chr2-198349536;