3-65114483-T-C

Variant names:

• chr3-65114483-T-C
• rs2128404
• ENST00000759543.1:n.436-5561A>G

Variant summary

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

The ENST00000759543.1(ENSG00000298971):​n.436-5561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,086 control chromosomes in the GnomAD database, including 9,457 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 0.35 (9457 hom., cov: 32)
• Consequence: ENSG00000298971 ENST00000759543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 4 publications found

Genes affected

ENSG00000298971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377125	XR_940925.3	n.125+547A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298971	ENST00000759543.1	n.436-5561A>G		intron_variant	Intron 3 of 4
ENSG00000298971	ENST00000759544.1	n.634-5561A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52882 AN: 151968 Hom.: 9449 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.348 AC: 52904 AN: 152086 Hom.: 9457 Cov.: 32 AF XY: 0.337 AC XY: 25057 AN XY: 74360

African (AFR) AF: 0.338 AC: 14030 AN: 41466

American (AMR) AF: 0.294 AC: 4493 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3466

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5166

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4814

European-Finnish (FIN) AF: 0.197 AC: 2085 AN: 10598

Middle Eastern (MID) AF: 0.448 AC: 130 AN: 290

European-Non Finnish (NFE) AF: 0.386 AC: 26253 AN: 67986

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.340 Hom.: 3352

Bravo AF: 0.356

Asia WGS AF: 0.340 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.5
DANN	Benign	0.81
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs2128404; hg19: chr3-65100158;