rs6750486

Variant names:

• chr2-35301852-C-T
• rs6750486

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 0.124 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
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.305 AC: 12386 AN: 40594

American (AMR) AF: 0.0727 AC: 1082 AN: 14884

Ashkenazi Jewish (ASJ) AF: 0.0289 AC: 100 AN: 3466

East Asian (EAS) AF: 0.109 AC: 556 AN: 5082

South Asian (SAS) AF: 0.0897 AC: 424 AN: 4728

European-Finnish (FIN) AF: 0.0511 AC: 510 AN: 9984

Middle Eastern (MID) AF: 0.0660 AC: 19 AN: 288

European-Non Finnish (NFE) AF: 0.0475 AC: 3218 AN: 67718

Other (OTH) AF: 0.107 AC: 224 AN: 2090

Alfa AF: 0.0660 Hom.: 1560

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6750486; hg19: chr2-35526918;