rs6759330

Variant names:

• chr2-138623096-G-A
• rs6759330

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 0.451 in 151,610 control chromosomes in the GnomAD database, including 18,849 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 0.45 (18849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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: 0.451 AC: 68305 AN: 151492 Hom.: 18806 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.451 AC: 68400 AN: 151610 Hom.: 18849 Cov.: 31 AF XY: 0.453 AC XY: 33572 AN XY: 74058

African (AFR) AF: 0.767 AC: 31777 AN: 41428

American (AMR) AF: 0.503 AC: 7633 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1401 AN: 3448

East Asian (EAS) AF: 0.458 AC: 2346 AN: 5126

South Asian (SAS) AF: 0.406 AC: 1944 AN: 4790

European-Finnish (FIN) AF: 0.298 AC: 3133 AN: 10504

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.277 AC: 18813 AN: 67822

Other (OTH) AF: 0.453 AC: 954 AN: 2108

Alfa AF: 0.339 Hom.: 43456

Bravo AF: 0.482

Asia WGS AF: 0.445 AC: 1551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.18
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6759330; hg19: chr2-139380666;