rs2523790

Variant names:

• chr6-29835873-T-G
• rs2523790

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 0.387 in 151,942 control chromosomes in the GnomAD database, including 12,348 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 0.39 (12348 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.386 AC: 58659 AN: 151824 Hom.: 12321 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.387 AC: 58739 AN: 151942 Hom.: 12348 Cov.: 31 AF XY: 0.388 AC XY: 28819 AN XY: 74278

African (AFR) AF: 0.530 AC: 21917 AN: 41378

American (AMR) AF: 0.461 AC: 7045 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3468

East Asian (EAS) AF: 0.512 AC: 2646 AN: 5168

South Asian (SAS) AF: 0.505 AC: 2426 AN: 4804

European-Finnish (FIN) AF: 0.241 AC: 2547 AN: 10584

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19603 AN: 67958

Other (OTH) AF: 0.418 AC: 881 AN: 2108

Alfa AF: 0.352 Hom.: 11000

Bravo AF: 0.408

Asia WGS AF: 0.585 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	4.9
DANN	Benign	0.37
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2523790; hg19: chr6-29803650;