6-14636732-T-C

Position:

• chr6-14636732-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702111.1(ENSG00000289958):​n.156+7219A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,180 control chromosomes in the GnomAD database, including 47,369 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 0.75 (47369 hom., cov: 32)
• Consequence: ENSG00000289958 ENST00000702111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899

Genes affected

ENSG00000289958 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928354	XR_001743992.2	n.303+5430A>G		intron_variant
LOC101928354	XR_007059472.1	n.225+7219A>G		intron_variant
LOC101928354	XR_241980.4	n.165+7219A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289958	ENST00000702111.1	n.156+7219A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113617 AN: 152062 Hom.: 47372 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.747 AC: 113639 AN: 152180 Hom.: 47369 Cov.: 32 AF XY: 0.751 AC XY: 55910 AN XY: 74414

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.778

Alfa AF: 0.873 Hom.: 86141

Bravo AF: 0.723

Asia WGS AF: 0.880 AC: 3060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs707824; hg19: chr6-14636963;