rs17149106

Variant names:

• chr7-24283588-G-A
• rs17149106
• ENST00000746097.1:n.346C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-24283588-G-A
• chr7-24283588-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000746097.1(ENSG00000297196):​n.346C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ENSG00000297196 ENST00000746097.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 18 publications found

Genes affected

ENSG00000297196 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+35769C>T		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-86559C>T		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+35769C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297196	ENST00000746097.1	n.346C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297196	ENST00000746098.1	n.401C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000228944	ENST00000718234.1	n.319+35769C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 14

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.45
DANN	Benign	0.62
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17149106; hg19: chr7-24323207;