8-79327412-A-G

Variant names:

• chr8-79327412-A-G
• rs1460167
• ENST00000765366.1:n.195+3450T>C

Variant summary

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

The ENST00000765366.1(ENSG00000299650):​n.195+3450T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,934 control chromosomes in the GnomAD database, including 10,377 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 0.34 (10377 hom., cov: 32)
• Consequence: ENSG00000299650 ENST00000765366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 2 publications found

Genes affected

ENSG00000299650 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765366.1. 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
	ENSG00000299650	ENST00000765366.1		n.195+3450T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52194 AN: 151814 Hom.: 10362 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.344 AC: 52249 AN: 151934 Hom.: 10377 Cov.: 32 AF XY: 0.344 AC XY: 25509 AN XY: 74252

African (AFR) AF: 0.492 AC: 20376 AN: 41406

American (AMR) AF: 0.342 AC: 5219 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1434 AN: 3464

East Asian (EAS) AF: 0.690 AC: 3553 AN: 5148

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1441 AN: 10582

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17272 AN: 67948

Other (OTH) AF: 0.378 AC: 796 AN: 2106

Alfa AF: 0.299 Hom.: 1335

Bravo AF: 0.366

Asia WGS AF: 0.574 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1460167; hg19: chr8-80239647;