rs6924119

Positions:

• chr6-14676739-C-T

Variant summary

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

The ENST00000629853.2(ENSG00000234261):​n.314-14446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,018 control chromosomes in the GnomAD database, including 2,387 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 0.099 (2387 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000629853.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928354	XR_001743992.2	n.47-32670G>A		intron_variant
LOC101928354	XR_241980.4	n.47-32670G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234261	ENST00000629853.2	n.314-14446G>A		intron_variant		5
ENSG00000234261	ENST00000689305.1	n.231-14446G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0992 AC: 15063 AN: 151900 Hom.: 2378 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.00982

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00451

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0994 AC: 15109 AN: 152018 Hom.: 2387 Cov.: 32 AF XY: 0.0954 AC XY: 7091 AN XY: 74336

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.00982

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00451

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0590 Hom.: 180

Bravo AF: 0.114

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6924119; hg19: chr6-14676970;