ENST00000808832.1:n.164-26533G>A

Variant names:

• chr4-12497263-C-T
• rs7665957
• ENST00000808832.1:n.164-26533G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000808832.1(ENSG00000305112):​n.164-26533G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 151,346 control chromosomes in the GnomAD database, including 45 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 0.014 (45 hom., cov: 32)
• Consequence: ENSG00000305112 ENST00000808832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 1 publications found

Genes affected

ENSG00000305112 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.014 (2118/151346) while in subpopulation AFR AF = 0.0481 (1984/41276). AF 95% confidence interval is 0.0463. There are 45 homozygotes in GnomAd4. There are 1007 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808832.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305112	ENST00000808832.1		n.164-26533G>A		intron	N/A
	ENSG00000305112	ENST00000808833.1		n.348-26533G>A		intron	N/A
	ENSG00000305112	ENST00000808834.1		n.264-26533G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2114 AN: 151228 Hom.: 45 Cov.: 32

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00609

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000280

Gnomad OTH AF: 0.0106

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

GnomAD4 genome AF: 0.0140 AC: 2118 AN: 151346 Hom.: 45 Cov.: 32 AF XY: 0.0136 AC XY: 1007 AN XY: 73840

African (AFR) AF: 0.0481 AC: 1984 AN: 41276

American (AMR) AF: 0.00608 AC: 92 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5084

South Asian (SAS) AF: 0.00 AC: 0 AN: 4798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10458

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.000280 AC: 19 AN: 67842

Other (OTH) AF: 0.0105 AC: 22 AN: 2098

Alfa AF: 0.0129 Hom.: 33

Bravo AF: 0.0163

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7665957; hg19: chr4-12498887;