rs4497633

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000275016 (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 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	ENST00000614344.5	n.193+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

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;