ENST00000805775.1:n.231+4675A>G

Variant names:

• chr7-113009359-A-G
• rs6969802
• ENST00000805775.1:n.231+4675A>G

Variant summary

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

The ENST00000805775.1(ENSG00000304714):​n.231+4675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,182 control chromosomes in the GnomAD database, including 1,896 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 0.13 (1896 hom., cov: 31)
• Consequence: ENSG00000304714 ENST00000805775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 2 publications found

Genes affected

ENSG00000304714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805775.1. 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
	ENSG00000304714	ENST00000805775.1		n.231+4675A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20341 AN: 152064 Hom.: 1894 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0910

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.134 AC: 20363 AN: 152182 Hom.: 1896 Cov.: 31 AF XY: 0.130 AC XY: 9687 AN XY: 74410

African (AFR) AF: 0.258 AC: 10690 AN: 41482

American (AMR) AF: 0.108 AC: 1654 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0910 AC: 316 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.158 AC: 762 AN: 4824

European-Finnish (FIN) AF: 0.0613 AC: 650 AN: 10606

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0863 AC: 5870 AN: 68006

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.114 Hom.: 164

Bravo AF: 0.142

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.4
DANN	Benign	0.66
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs6969802; hg19: chr7-112649414;