rs2859338

Variant names:

• chr6-12298751-G-A
• rs2859338
• ENST00000789274.1:n.1103-2262C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789274.1(ENSG00000302734):​n.1103-2262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,144 control chromosomes in the GnomAD database, including 8,685 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 0.30 (8685 hom., cov: 33)
• Consequence: ENSG00000302734 ENST00000789274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 10 publications found

Genes affected

ENSG00000302734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789274.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302734	ENST00000789274.1		n.1103-2262C>T		intron	N/A
	ENSG00000302734	ENST00000789275.1		n.704-2262C>T		intron	N/A
	ENSG00000302734	ENST00000789276.1		n.1706-2262C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45318 AN: 152026 Hom.: 8688 Cov.: 33

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.298 AC: 45308 AN: 152144 Hom.: 8685 Cov.: 33 AF XY: 0.295 AC XY: 21933 AN XY: 74362

African (AFR) AF: 0.0769 AC: 3192 AN: 41534

American (AMR) AF: 0.312 AC: 4772 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1306 AN: 3468

East Asian (EAS) AF: 0.0386 AC: 200 AN: 5186

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4828

European-Finnish (FIN) AF: 0.418 AC: 4408 AN: 10556

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29172 AN: 67980

Other (OTH) AF: 0.317 AC: 668 AN: 2110

Alfa AF: 0.377 Hom.: 38262

Bravo AF: 0.279

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.9
DANN	Benign	0.69
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2859338; hg19: chr6-12298984;