chr17-32436776-A-G

Variant names:

• chr17-32436776-A-G
• rs4795700
• ENST00000623710.1:n.288-371T>C

Variant summary

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

The ENST00000623710.1(ENSG00000279762):​n.288-371T>C variant causes a intron 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: ENSG00000279762 ENST00000623710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 14 publications found

Genes affected

ENSG00000279762 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279762	ENST00000623710.1	n.288-371T>C		intron_variant	Intron 1 of 2	5
ENSG00000279762	ENST00000625127.3	n.2810+1698T>C		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.731 AC: 30312 AN: 41474

American (AMR) AF: 0.534 AC: 8157 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2130 AN: 3470

East Asian (EAS) AF: 0.0995 AC: 516 AN: 5186

South Asian (SAS) AF: 0.501 AC: 2405 AN: 4804

European-Finnish (FIN) AF: 0.652 AC: 6889 AN: 10558

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41450 AN: 67968

Other (OTH) AF: 0.581 AC: 1228 AN: 2112

Alfa AF: 0.589 Hom.: 21961

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4795700; hg19: chr17-30763794;