rs156243

Variant names:

• chr6-104416939-G-A
• rs156243
• ENST00000790145.1:n.408+5006G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-104416939-G-A
• chr6-104416939-G-C
• chr6-104416939-G-T

Variant summary

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

The ENST00000790145.1(ENSG00000302865):​n.408+5006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,444 control chromosomes in the GnomAD database, including 37,479 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 0.66 (37479 hom., cov: 28)
• Consequence: ENSG00000302865 ENST00000790145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 2 publications found

Genes affected

ENSG00000302865 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 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
ENSG00000302865	ENST00000790145.1	n.408+5006G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99442 AN: 151326 Hom.: 37478 Cov.: 28

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.657 AC: 99460 AN: 151444 Hom.: 37479 Cov.: 28 AF XY: 0.658 AC XY: 48702 AN XY: 73980

African (AFR) AF: 0.253 AC: 10410 AN: 41190

American (AMR) AF: 0.758 AC: 11525 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2653 AN: 3468

East Asian (EAS) AF: 0.707 AC: 3623 AN: 5126

South Asian (SAS) AF: 0.785 AC: 3770 AN: 4804

European-Finnish (FIN) AF: 0.812 AC: 8484 AN: 10444

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56682 AN: 67900

Other (OTH) AF: 0.683 AC: 1441 AN: 2110

Alfa AF: 0.770 Hom.: 10300

Bravo AF: 0.633

Asia WGS AF: 0.723 AC: 2511 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.54
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs156243; hg19: chr6-104864814; COSMIC: COSV69418783;