3-65162946-G-A

Variant names:

• chr3-65162946-G-A
• rs10510933
• ENST00000759543.1:n.435+2493C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000759543.1(ENSG00000298971):​n.435+2493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,948 control chromosomes in the GnomAD database, including 2,739 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 0.18 (2739 hom., cov: 32)
• Consequence: ENSG00000298971 ENST00000759543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 3 publications found

Genes affected

ENSG00000298971 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377127	XR_001740735.2	n.1430-1233C>T		intron_variant	Intron 4 of 4
LOC105377127	XR_001740736.1	n.590-1233C>T		intron_variant	Intron 3 of 3
LOC105377127	XR_940926.3	n.1097-1233C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298971	ENST00000759543.1	n.435+2493C>T		intron_variant	Intron 3 of 4
ENSG00000298971	ENST00000759544.1	n.633+2493C>T		intron_variant	Intron 3 of 4
ENSG00000298971	ENST00000759545.1	n.441-1233C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27532 AN: 151830 Hom.: 2739 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.181 AC: 27537 AN: 151948 Hom.: 2739 Cov.: 32 AF XY: 0.188 AC XY: 13976 AN XY: 74272

African (AFR) AF: 0.118 AC: 4892 AN: 41482

American (AMR) AF: 0.154 AC: 2355 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1300 AN: 5140

South Asian (SAS) AF: 0.205 AC: 989 AN: 4820

European-Finnish (FIN) AF: 0.335 AC: 3535 AN: 10540

Middle Eastern (MID) AF: 0.266 AC: 77 AN: 290

European-Non Finnish (NFE) AF: 0.195 AC: 13230 AN: 67922

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.183 Hom.: 5173

Bravo AF: 0.166

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10510933; hg19: chr3-65148621;