3-72466809-G-A

Variant names:

• chr3-72466809-G-A
• rs11128275
• ENST00000810549.1:n.412+7684G>A

Variant summary

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

The ENST00000810549.1(ENSG00000305353):​n.412+7684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,006 control chromosomes in the GnomAD database, including 17,548 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 (17548 hom., cov: 32)
• Consequence: ENSG00000305353 ENST00000810549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 4 publications found

Genes affected

ENSG00000305353 (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 = 0.686 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
ENSG00000305353	ENST00000810549.1	n.412+7684G>A		intron_variant	Intron 2 of 2
ENSG00000305353	ENST00000810550.1	n.371+7684G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69225 AN: 151888 Hom.: 17534 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.456 AC: 69253 AN: 152006 Hom.: 17548 Cov.: 32 AF XY: 0.465 AC XY: 34554 AN XY: 74280

African (AFR) AF: 0.224 AC: 9302 AN: 41458

American (AMR) AF: 0.569 AC: 8683 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1565 AN: 3466

East Asian (EAS) AF: 0.705 AC: 3644 AN: 5168

South Asian (SAS) AF: 0.602 AC: 2903 AN: 4822

European-Finnish (FIN) AF: 0.565 AC: 5961 AN: 10544

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35629 AN: 67984

Other (OTH) AF: 0.461 AC: 969 AN: 2104

Alfa AF: 0.497 Hom.: 22703

Bravo AF: 0.447

Asia WGS AF: 0.591 AC: 2054 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	0.24
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11128275; hg19: chr3-72515960;