rs4497633

Variant names:

• chr15-95647302-C-T
• rs4497633
• ENST00000611285.1:n.26+8783C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000611285.1(ENSG00000275016):​n.26+8783C>T variant causes a intron 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: ENSG00000275016 ENST00000611285.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 1 publications found

Genes affected

ENSG00000275016 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275016	ENST00000611285.1	n.26+8783C>T		intron_variant	Intron 1 of 1	5
ENSG00000275016	ENST00000612595.2	n.204+8783C>T		intron_variant	Intron 1 of 2	5
ENSG00000275016	ENST00000614344.6	n.201+8783C>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.113 AC: 4702 AN: 41534

American (AMR) AF: 0.159 AC: 2429 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3464

East Asian (EAS) AF: 0.168 AC: 873 AN: 5188

South Asian (SAS) AF: 0.119 AC: 574 AN: 4832

European-Finnish (FIN) AF: 0.0460 AC: 487 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0220 AC: 1494 AN: 68018

Other (OTH) AF: 0.0766 AC: 162 AN: 2116

Alfa AF: 0.0469 Hom.: 667

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4497633; hg19: chr15-96190531;