ENST00000577647.2:n.*2199+391T>C

Variant names:

• chr17-63520757-T-C
• rs4968591
• ENST00000577647.2:n.*2199+391T>C

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.*2199+391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,172 control chromosomes in the GnomAD database, including 8,828 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 0.32 (8828 hom., cov: 33)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 12 publications found

Genes affected

ENSG00000264813 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 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
ENSG00000264813	ENST00000577647.2	n.*2199+391T>C		intron_variant	Intron 29 of 30	2		ENSP00000464149.1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48916 AN: 152054 Hom.: 8828 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.321 AC: 48915 AN: 152172 Hom.: 8828 Cov.: 33 AF XY: 0.319 AC XY: 23704 AN XY: 74386

African (AFR) AF: 0.158 AC: 6551 AN: 41514

American (AMR) AF: 0.329 AC: 5032 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1645 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5184

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4814

European-Finnish (FIN) AF: 0.365 AC: 3857 AN: 10576

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27855 AN: 68010

Other (OTH) AF: 0.362 AC: 763 AN: 2108

Alfa AF: 0.363 Hom.: 6145

Bravo AF: 0.311

Asia WGS AF: 0.205 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4968591; hg19: chr17-61598118;