rs4575595

Variant names:

• chr17-63499854-G-A
• rs4575595
• ENST00000577647.2:n.1969+2869G>A

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.1969+2869G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,158 control chromosomes in the GnomAD database, including 15,051 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 0.43 (15051 hom., cov: 34)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 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.1969+2869G>A		intron_variant	Intron 13 of 30	2		ENSP00000464149.1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65814 AN: 152042 Hom.: 15024 Cov.: 34

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.433 AC: 65855 AN: 152158 Hom.: 15051 Cov.: 34 AF XY: 0.437 AC XY: 32506 AN XY: 74384

African (AFR) AF: 0.279 AC: 11586 AN: 41530

American (AMR) AF: 0.505 AC: 7731 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3007 AN: 5160

South Asian (SAS) AF: 0.583 AC: 2813 AN: 4826

European-Finnish (FIN) AF: 0.484 AC: 5114 AN: 10574

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33028 AN: 67986

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.457 Hom.: 2046

Bravo AF: 0.422

Asia WGS AF: 0.617 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.1
DANN	Benign	0.76
PhyloP100		1.0
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: rs4575595; hg19: chr17-61577215;