3-72484093-T-C

Variant names:

• chr3-72484093-T-C
• rs6775777
• ENST00000810476.1:n.225-11341A>G

Variant summary

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

The ENST00000810476.1(ENSG00000244345):​n.225-11341A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 151,246 control chromosomes in the GnomAD database, including 51,162 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 0.82 (51162 hom., cov: 26)
• Consequence: ENSG00000244345 ENST00000810476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 2 publications found

Genes affected

ENSG00000244345 (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 (EAS) allele frequency at 95% confidence interval = 0.87 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
ENSG00000244345	ENST00000810476.1	n.225-11341A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.818 AC: 123616 AN: 151130 Hom.: 51142 Cov.: 26

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.818 AC: 123686 AN: 151246 Hom.: 51162 Cov.: 26 AF XY: 0.822 AC XY: 60752 AN XY: 73866

African (AFR) AF: 0.678 AC: 27834 AN: 41042

American (AMR) AF: 0.865 AC: 13127 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2904 AN: 3466

East Asian (EAS) AF: 0.891 AC: 4569 AN: 5126

South Asian (SAS) AF: 0.872 AC: 4179 AN: 4792

European-Finnish (FIN) AF: 0.918 AC: 9592 AN: 10448

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.866 AC: 58800 AN: 67900

Other (OTH) AF: 0.802 AC: 1682 AN: 2098

Alfa AF: 0.823 Hom.: 7420

Bravo AF: 0.811

Asia WGS AF: 0.867 AC: 3015 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	1.1
DANN	Benign	0.79
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6775777; hg19: chr3-72533244;