rs4497633

Positions:

• chr15-95647302-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000612595.2(ENSG00000275016):​n.204+8783C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,248 control chromosomes in the GnomAD database, including 683 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 0.071 (683 hom., cov: 34)
• Consequence: ENST00000612595.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000612595.2	n.204+8783C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10728 AN: 152130 Hom.: 674 Cov.: 34

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0460

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0707 AC: 10767 AN: 152248 Hom.: 683 Cov.: 34 AF XY: 0.0742 AC XY: 5524 AN XY: 74442

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0460

Gnomad4 NFE AF: 0.0220

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0595 Hom.: 128

Bravo AF: 0.0850

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	19
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4497633; hg19: chr15-96190531;