ENST00000807975.1:n.60-1568T>C

Variant names:

• chr3-143186819-A-G
• rs6776634
• ENST00000807975.1:n.60-1568T>C

Variant summary

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

The ENST00000807975.1(ENSG00000305033):​n.60-1568T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,080 control chromosomes in the GnomAD database, including 42,864 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 0.75 (42864 hom., cov: 31)
• Consequence: ENSG00000305033 ENST00000807975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 3 publications found

Genes affected

ENSG00000305033 (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 = 0.826 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
ENSG00000305033	ENST00000807975.1	n.60-1568T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113515 AN: 151962 Hom.: 42823 Cov.: 31

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.747 AC: 113607 AN: 152080 Hom.: 42864 Cov.: 31 AF XY: 0.744 AC XY: 55307 AN XY: 74350

African (AFR) AF: 0.833 AC: 34545 AN: 41476

American (AMR) AF: 0.739 AC: 11288 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2196 AN: 3466

East Asian (EAS) AF: 0.784 AC: 4055 AN: 5172

South Asian (SAS) AF: 0.557 AC: 2688 AN: 4824

European-Finnish (FIN) AF: 0.737 AC: 7790 AN: 10572

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48673 AN: 67982

Other (OTH) AF: 0.729 AC: 1536 AN: 2106

Alfa AF: 0.723 Hom.: 51492

Bravo AF: 0.760

Asia WGS AF: 0.670 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6776634; hg19: chr3-142905661;