rs4575595

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000264813 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.409

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4575595; hg19: chr17-61577215;