15-64895021-T-C

Variant names:

• chr15-64895021-T-C
• rs1628955
• ENST00000437723.1:c.484-26900T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000437723.1(ENSG00000249240):​c.484-26900T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,068 control chromosomes in the GnomAD database, including 40,633 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 (40633 hom., cov: 31)
• Consequence: ENSG00000249240 ENST00000437723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

Genes affected

ENSG00000249240 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.92 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
ENSG00000249240	ENST00000437723.1	c.484-26900T>C		intron_variant	Intron 5 of 6	5		ENSP00000397942.1
ENSG00000249240	ENST00000502574.1	n.618-26900T>C		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109397 AN: 151950 Hom.: 40580 Cov.: 31

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.720 AC: 109508 AN: 152068 Hom.: 40633 Cov.: 31 AF XY: 0.723 AC XY: 53691 AN XY: 74302

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.697

Alfa AF: 0.653 Hom.: 14974

Bravo AF: 0.736

Asia WGS AF: 0.888 AC: 3088 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	5.0
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1628955; hg19: chr15-65187220;