ENST00000780278.1:n.131+9319T>C

Variant names:

• chr15-36352187-A-G
• rs7178364
• ENST00000780278.1:n.131+9319T>C

Variant summary

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

The ENST00000780278.1(ENSG00000301624):​n.131+9319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,040 control chromosomes in the GnomAD database, including 13,352 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 0.39 (13352 hom., cov: 32)
• Consequence: ENSG00000301624 ENST00000780278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 1 publications found

Genes affected

ENSG00000301624 (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 (AMR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370767	XR_932108.3	n.275+9053T>C		intron_variant	Intron 1 of 1
LOC105370767	XR_932109.2	n.301+7360T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301624	ENST00000780278.1	n.131+9319T>C		intron_variant	Intron 2 of 2
ENSG00000301624	ENST00000780279.1	n.275+9053T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59321 AN: 151922 Hom.: 13353 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.390 AC: 59329 AN: 152040 Hom.: 13352 Cov.: 32 AF XY: 0.391 AC XY: 29028 AN XY: 74322

African (AFR) AF: 0.173 AC: 7180 AN: 41482

American (AMR) AF: 0.527 AC: 8047 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2041 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5174

South Asian (SAS) AF: 0.385 AC: 1855 AN: 4824

European-Finnish (FIN) AF: 0.391 AC: 4127 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33019 AN: 67964

Other (OTH) AF: 0.424 AC: 892 AN: 2106

Alfa AF: 0.432 Hom.: 3379

Bravo AF: 0.391

Asia WGS AF: 0.327 AC: 1136 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7178364; hg19: chr15-36644388;