rs17045031

Variant names:

• chr3-66717940-G-A
• rs17045031
• ENST00000735387.1:n.253C>T

Variant summary

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

The ENST00000735379.1(ENSG00000296009):​n.185+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 152,126 control chromosomes in the GnomAD database, including 1,505 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 0.097 (1505 hom., cov: 32)
• Consequence: ENSG00000296009 ENST00000735379.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 10 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735379.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296009	ENST00000735387.1		n.253C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000296009	ENST00000735389.1		n.249C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000296009	ENST00000735379.1		n.185+4C>T		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0970 AC: 14740 AN: 152008 Hom.: 1499 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0585

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.0970 AC: 14763 AN: 152126 Hom.: 1505 Cov.: 32 AF XY: 0.0950 AC XY: 7068 AN XY: 74378

African (AFR) AF: 0.262 AC: 10860 AN: 41446

American (AMR) AF: 0.0584 AC: 893 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4816

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0347 AC: 2362 AN: 68026

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0544 Hom.: 1869

Bravo AF: 0.109

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.58
PhyloP100		-0.86

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17045031;

hg19: chr3-66768364;