15-95887405-T-C

Variant names:

• chr15-95887405-T-C
• rs725213
• ENST00000767924.1:n.401A>G

Variant summary

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

The ENST00000767924.1(ENSG00000300007):​n.401A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,098 control chromosomes in the GnomAD database, including 40,207 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 0.72 (40207 hom., cov: 32)
• Consequence: ENSG00000300007 ENST00000767924.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 4 publications found

Genes affected

ENSG00000300007 (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 (EAS) allele frequency at 95% confidence interval = 0.856 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
ENSG00000300007	ENST00000767924.1	n.401A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000300007	ENST00000767921.1	n.471+663A>G		intron_variant	Intron 3 of 3
ENSG00000300007	ENST00000767922.1	n.304+663A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109869 AN: 151980 Hom.: 40147 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.723 AC: 109984 AN: 152098 Hom.: 40207 Cov.: 32 AF XY: 0.725 AC XY: 53868 AN XY: 74338

African (AFR) AF: 0.818 AC: 33945 AN: 41504

American (AMR) AF: 0.711 AC: 10867 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2639 AN: 3468

East Asian (EAS) AF: 0.878 AC: 4533 AN: 5164

South Asian (SAS) AF: 0.722 AC: 3480 AN: 4820

European-Finnish (FIN) AF: 0.594 AC: 6263 AN: 10552

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45877 AN: 67988

Other (OTH) AF: 0.746 AC: 1576 AN: 2112

Alfa AF: 0.694 Hom.: 62854

Bravo AF: 0.737

Asia WGS AF: 0.767 AC: 2668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.64
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs725213; hg19: chr15-96430634;