ENST00000795608.1:n.633-71C>T

Variant names:

• chr15-40964568-C-T
• rs1869907
• ENST00000795608.1:n.633-71C>T

Variant summary

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

The ENST00000795608.1(ENSG00000303560):​n.633-71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,594 control chromosomes in the GnomAD database, including 19,807 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 0.50 (19807 hom., cov: 29)
• Consequence: ENSG00000303560 ENST00000795608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 10 publications found

Genes affected

ENSG00000303560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795608.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303560	ENST00000795608.1		n.633-71C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76226 AN: 151476 Hom.: 19802 Cov.: 29

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.503 AC: 76250 AN: 151594 Hom.: 19807 Cov.: 29 AF XY: 0.509 AC XY: 37661 AN XY: 74056

African (AFR) AF: 0.371 AC: 15309 AN: 41308

American (AMR) AF: 0.558 AC: 8512 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3506 AN: 5122

South Asian (SAS) AF: 0.472 AC: 2259 AN: 4788

European-Finnish (FIN) AF: 0.649 AC: 6816 AN: 10510

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36367 AN: 67844

Other (OTH) AF: 0.502 AC: 1058 AN: 2106

Alfa AF: 0.517 Hom.: 26033

Bravo AF: 0.494

Asia WGS AF: 0.546 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.66
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1869907; hg19: chr15-41256766;