chr15-26097593-T-G

Variant names:

• chr15-26097593-T-G
• rs1006179
• ENST00000777844.1:n.618-7618A>C

Variant summary

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

The ENST00000777844.1(ENSG00000301308):​n.618-7618A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,230 control chromosomes in the GnomAD database, including 2,145 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 0.13 (2145 hom., cov: 32)
• Consequence: ENSG00000301308 ENST00000777844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 0 publications found

Genes affected

ENSG00000301308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777844.1. 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
	ENSG00000301308	ENST00000777844.1		n.618-7618A>C		intron	N/A
	ENSG00000301308	ENST00000777845.1		n.221-7618A>C		intron	N/A
	ENSG00000301324	ENST00000778012.1		n.606+17T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19423 AN: 152112 Hom.: 2132 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0691

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.128 AC: 19483 AN: 152230 Hom.: 2145 Cov.: 32 AF XY: 0.132 AC XY: 9796 AN XY: 74432

African (AFR) AF: 0.272 AC: 11288 AN: 41522

American (AMR) AF: 0.115 AC: 1766 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0691 AC: 240 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1527 AN: 5168

South Asian (SAS) AF: 0.222 AC: 1069 AN: 4816

European-Finnish (FIN) AF: 0.0404 AC: 429 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0424 AC: 2881 AN: 68014

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.0731 Hom.: 2246

Bravo AF: 0.137

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.37
PhyloP100		0.095

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: rs1006179;

hg19: chr15-26342740;