3-66703250-C-T

Variant names:

• chr3-66703250-C-T
• rs11710109
• ENST00000735379.1:n.186-2065G>A

Variant summary

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

The ENST00000735379.1(ENSG00000296009):​n.186-2065G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,000 control chromosomes in the GnomAD database, including 17,449 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 (17449 hom., cov: 32)
• Consequence: ENSG00000296009 ENST00000735379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 3 publications found

Genes affected

ENSG00000296009 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377142	XR_940935.3	n.186-2065G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296009	ENST00000735379.1	n.186-2065G>A		intron_variant	Intron 2 of 3
ENSG00000296009	ENST00000735381.1	n.289-2065G>A		intron_variant	Intron 2 of 2
ENSG00000296009	ENST00000735382.1	n.296-2065G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70616 AN: 151882 Hom.: 17432 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.465 AC: 70670 AN: 152000 Hom.: 17449 Cov.: 32 AF XY: 0.463 AC XY: 34422 AN XY: 74280

African (AFR) AF: 0.642 AC: 26620 AN: 41452

American (AMR) AF: 0.342 AC: 5216 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3002 AN: 5146

South Asian (SAS) AF: 0.278 AC: 1338 AN: 4816

European-Finnish (FIN) AF: 0.435 AC: 4602 AN: 10572

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26851 AN: 67970

Other (OTH) AF: 0.449 AC: 950 AN: 2114

Alfa AF: 0.416 Hom.: 37450

Bravo AF: 0.471

Asia WGS AF: 0.408 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.77
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs11710109; hg19: chr3-66753674;