rs723142

Variant names:

• chr6-82327838-T-C
• rs723142
• ENST00000847264.1:n.145-6756A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-82327838-T-C
• chr6-82327838-T-G

Variant summary

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

The ENST00000847264.1(ENSG00000286875):​n.145-6756A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,980 control chromosomes in the GnomAD database, including 35,718 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 0.68 (35718 hom., cov: 32)
• Consequence: ENSG00000286875 ENST00000847264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 2 publications found

Genes affected

ENSG00000286875 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.684 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
ENSG00000286875	ENST00000847264.1	n.145-6756A>G		intron_variant	Intron 1 of 3
ENSG00000286875	ENST00000847265.1	n.158-6756A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103821 AN: 151862 Hom.: 35683 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.684 AC: 103915 AN: 151980 Hom.: 35718 Cov.: 32 AF XY: 0.688 AC XY: 51067 AN XY: 74256

African (AFR) AF: 0.671 AC: 27800 AN: 41432

American (AMR) AF: 0.691 AC: 10538 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2283 AN: 3464

East Asian (EAS) AF: 0.587 AC: 3033 AN: 5170

South Asian (SAS) AF: 0.701 AC: 3378 AN: 4816

European-Finnish (FIN) AF: 0.725 AC: 7669 AN: 10582

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46834 AN: 67948

Other (OTH) AF: 0.721 AC: 1523 AN: 2112

Alfa AF: 0.681 Hom.: 4404

Bravo AF: 0.683

Asia WGS AF: 0.666 AC: 2305 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs723142; hg19: chr6-83037555;