rs1396669

Variant names:

• chr4-23343831-T-A
• rs1396669
• ENST00000757640.1:n.285-14388A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-23343831-T-A
• chr4-23343831-T-G

Variant summary

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

The ENST00000757640.1(ENSG00000298732):​n.285-14388A>T variant causes a intron 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: ENSG00000298732 ENST00000757640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 4 publications found

Genes affected

ENSG00000298732 (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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374523	XR_001741614.1	n.227-14388A>T		intron_variant	Intron 1 of 2
LOC105374524	XR_007058437.1	n.2932+10305T>A		intron_variant	Intron 16 of 18
LOC105374523	XR_925460.2	n.227-14388A>T		intron_variant	Intron 1 of 2
LOC105374523	XR_925461.2	n.266-14388A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298732	ENST00000757640.1	n.285-14388A>T		intron_variant	Intron 1 of 4
ENSG00000298732	ENST00000757641.1	n.268-14388A>T		intron_variant	Intron 1 of 3
ENSG00000298732	ENST00000757642.1	n.253-14388A>T		intron_variant	Intron 1 of 5

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.: 36308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.46
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1396669; hg19: chr4-23345454;