8-78091416-T-C

Variant names:

• chr8-78091416-T-C
• rs1994035
• ENST00000810365.1:n.438-8427T>C

Variant summary

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

The ENST00000810365.1(ENSG00000305312):​n.438-8427T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,664 control chromosomes in the GnomAD database, including 18,301 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 0.46 (18301 hom., cov: 31)
• Consequence: ENSG00000305312 ENST00000810365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 publications found

Genes affected

ENSG00000305312 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810365.1. 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
	ENSG00000305312	ENST00000810365.1		n.438-8427T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70253 AN: 151546 Hom.: 18262 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.464 AC: 70344 AN: 151664 Hom.: 18301 Cov.: 31 AF XY: 0.460 AC XY: 34061 AN XY: 74108

African (AFR) AF: 0.712 AC: 29474 AN: 41384

American (AMR) AF: 0.414 AC: 6285 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3466

East Asian (EAS) AF: 0.504 AC: 2582 AN: 5120

South Asian (SAS) AF: 0.461 AC: 2221 AN: 4814

European-Finnish (FIN) AF: 0.329 AC: 3462 AN: 10524

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23409 AN: 67856

Other (OTH) AF: 0.448 AC: 942 AN: 2102

Alfa AF: 0.412 Hom.: 2444

Bravo AF: 0.481

Asia WGS AF: 0.517 AC: 1790 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.032
DANN	Benign	0.60
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1994035; hg19: chr8-79003651; COSMIC: COSV64449526;