rs4267385

Variant names:

• chr17-63506395-C-T
• rs4267385
• ENST00000577647.2:n.1970-661C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577647.2(ENSG00000264813):​n.1970-661C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,860 control chromosomes in the GnomAD database, including 28,645 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 0.60 (28645 hom., cov: 31)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

Genes affected

ENSG00000264813 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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.1970-661C>T		intron_variant	Intron 13 of 30	2		ENSP00000464149.1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90959 AN: 151742 Hom.: 28605 Cov.: 31

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.600 AC: 91046 AN: 151860 Hom.: 28645 Cov.: 31 AF XY: 0.588 AC XY: 43635 AN XY: 74212

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.613

Alfa AF: 0.573 Hom.: 13687

Bravo AF: 0.608

Asia WGS AF: 0.344 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.36

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: rs4267385; hg19: chr17-61583756;