rs4795700

chr17-32436776-A-G

Variant summary

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

The ENST00000625127.3(ENSG00000279762):n.2810+1698T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,044 control chromosomes in the GnomAD database, including 30,068 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 0.62 (30068 hom., cov: 31)
• Consequence: ENST00000625127.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000625127.3	n.2810+1698T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000623710.1	n.288-371T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93701 AN: 151926 Hom.: 30022 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.617 AC: 93801 AN: 152044 Hom.: 30068 Cov.: 31 AF XY: 0.614 AC XY: 45604 AN XY: 74312

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.581

Alfa AF: 0.593 Hom.: 16059

Bravo AF: 0.610

Asia WGS AF: 0.338 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4795700; hg19: chr17-30763794;