rs6750486

Positions:

• chr2-35301852-C-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 0.124 in 149,744 control chromosomes in the GnomAD database, including 2,064 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 0.12 (2064 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18545 AN: 149636 Hom.: 2062 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0641

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.124 AC: 18578 AN: 149744 Hom.: 2064 Cov.: 30 AF XY: 0.123 AC XY: 8939 AN XY: 72908

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0289

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0897

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0572 Hom.: 709

Bravo AF: 0.132

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.6
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6750486; hg19: chr2-35526918;