rs6582709

Variant names:

• chr12-47424118-G-A
• rs6582709
• ENST00000848642.1:n.510+2750C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-47424118-G-A
• chr12-47424118-G-C

Variant summary

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

The ENST00000848642.1(ENSG00000310270):​n.510+2750C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,924 control chromosomes in the GnomAD database, including 17,675 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 0.47 (17675 hom., cov: 31)
• Consequence: ENSG00000310270 ENST00000848642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 3 publications found

Genes affected

ENSG00000310270 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848642.1. 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
	ENSG00000310270	ENST00000848642.1		n.510+2750C>T		intron	N/A
	ENSG00000310270	ENST00000848643.1		n.530+2750C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71054 AN: 151806 Hom.: 17637 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.468 AC: 71145 AN: 151924 Hom.: 17675 Cov.: 31 AF XY: 0.461 AC XY: 34198 AN XY: 74240

African (AFR) AF: 0.630 AC: 26085 AN: 41434

American (AMR) AF: 0.417 AC: 6360 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5166

South Asian (SAS) AF: 0.449 AC: 2163 AN: 4814

European-Finnish (FIN) AF: 0.336 AC: 3535 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28397 AN: 67926

Other (OTH) AF: 0.500 AC: 1053 AN: 2108

Alfa AF: 0.434 Hom.: 43767

Bravo AF: 0.476

Asia WGS AF: 0.420 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.2
DANN	Benign	0.91
PhyloP100		-0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6582709;

hg19: chr12-47817901;