6-14636732-T-G

Variant names:

• chr6-14636732-T-G
• rs707824
• ENST00000702111.1:n.156+7219A>C

Variant summary

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

The ENST00000702111.1(ENSG00000234261):​n.156+7219A>C 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: 32)
• Consequence: ENSG00000234261 ENST00000702111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 18 publications found

Genes affected

ENSG00000234261 (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=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928354	XR_001743992.2	n.303+5430A>C		intron_variant	Intron 3 of 4
LOC101928354	XR_007059472.1	n.225+7219A>C		intron_variant	Intron 2 of 3
LOC101928354	XR_241980.4	n.165+7219A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234261	ENST00000702111.1	n.156+7219A>C		intron_variant	Intron 2 of 2
ENSG00000234261	ENST00000729738.1	n.229+7219A>C		intron_variant	Intron 2 of 7
ENSG00000234261	ENST00000729739.1	n.165+7219A>C		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.83
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs707824; hg19: chr6-14636963;