15-69119630-T-C

Variant names:

• chr15-69119630-T-C
• rs11072067
• ENST00000822156.1:n.424+3959A>G

Variant summary

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

The ENST00000822156.1(ENSG00000306951):​n.424+3959A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,110 control chromosomes in the GnomAD database, including 30,821 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 0.63 (30821 hom., cov: 32)
• Consequence: ENSG00000306951 ENST00000822156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 1 publications found

Genes affected

ENSG00000306951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822156.1. 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
	ENSG00000306951	ENST00000822156.1		n.424+3959A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95113 AN: 151992 Hom.: 30804 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.626 AC: 95173 AN: 152110 Hom.: 30821 Cov.: 32 AF XY: 0.626 AC XY: 46544 AN XY: 74348

African (AFR) AF: 0.453 AC: 18787 AN: 41474

American (AMR) AF: 0.733 AC: 11210 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2367 AN: 3470

East Asian (EAS) AF: 0.605 AC: 3122 AN: 5160

South Asian (SAS) AF: 0.693 AC: 3336 AN: 4816

European-Finnish (FIN) AF: 0.637 AC: 6744 AN: 10588

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47466 AN: 67988

Other (OTH) AF: 0.659 AC: 1390 AN: 2108

Alfa AF: 0.677 Hom.: 102670

Bravo AF: 0.626

Asia WGS AF: 0.644 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.51

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: rs11072067;

hg19: chr15-69411969;