15-34675753-T-C

Variant names:

• chr15-34675753-T-C
• rs7170342
• ENST00000720751.1:n.235-120A>G

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.235-120A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,046 control chromosomes in the GnomAD database, including 32,937 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 0.65 (32937 hom., cov: 32)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 3 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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
ENSG00000294065	ENST00000720751.1	n.235-120A>G		intron_variant	Intron 1 of 1
ENSG00000287973	ENST00000720811.1	n.170-7043T>C		intron_variant	Intron 2 of 2
ENSG00000287973	ENST00000720812.1	n.281-7043T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98354 AN: 151928 Hom.: 32900 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.647 AC: 98437 AN: 152046 Hom.: 32937 Cov.: 32 AF XY: 0.638 AC XY: 47452 AN XY: 74322

African (AFR) AF: 0.801 AC: 33229 AN: 41480

American (AMR) AF: 0.491 AC: 7506 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2126 AN: 3462

East Asian (EAS) AF: 0.527 AC: 2727 AN: 5176

South Asian (SAS) AF: 0.508 AC: 2454 AN: 4834

European-Finnish (FIN) AF: 0.529 AC: 5590 AN: 10562

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

European-Non Finnish (NFE) AF: 0.627 AC: 42625 AN: 67938

Other (OTH) AF: 0.631 AC: 1331 AN: 2110

Alfa AF: 0.613 Hom.: 14623

Bravo AF: 0.651

Asia WGS AF: 0.512 AC: 1778 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7170342; hg19: chr15-34967954;