rs2705565

Variant names:

• chr3-112500489-C-T
• rs2705565
• ENST00000793585.1:n.393-17519C>T

Variant summary

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

The ENST00000793585.1(ENSG00000303317):​n.393-17519C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,974 control chromosomes in the GnomAD database, including 3,973 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 0.16 (3973 hom., cov: 32)
• Consequence: ENSG00000303317 ENST00000793585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 4 publications found

Genes affected

ENSG00000303317 (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 (AFR) allele frequency at 95% confidence interval = 0.41 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
ENSG00000303317	ENST00000793585.1	n.393-17519C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23934 AN: 151856 Hom.: 3968 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.158 AC: 23970 AN: 151974 Hom.: 3973 Cov.: 32 AF XY: 0.157 AC XY: 11668 AN XY: 74324

African (AFR) AF: 0.415 AC: 17154 AN: 41310

American (AMR) AF: 0.145 AC: 2223 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3472

East Asian (EAS) AF: 0.186 AC: 962 AN: 5172

South Asian (SAS) AF: 0.125 AC: 604 AN: 4820

European-Finnish (FIN) AF: 0.0255 AC: 270 AN: 10602

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2266 AN: 67998

Other (OTH) AF: 0.130 AC: 275 AN: 2112

Alfa AF: 0.120 Hom.: 448

Bravo AF: 0.181

Asia WGS AF: 0.139 AC: 483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.28
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs2705565; hg19: chr3-112219336;