6-14705946-A-G

Position:

• chr6-14705946-A-G

Variant summary

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

The ENST00000629853.2(ENSG00000234261):​n.314-43653T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,080 control chromosomes in the GnomAD database, including 40,853 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 0.68 (40853 hom., cov: 32)
• Consequence: ENST00000629853.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928354	XR_241980.4	n.46+11498T>C		intron_variant, non_coding_transcript_variant
LOC101928354	XR_001743992.2	n.46+11498T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000629853.2	n.314-43653T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000689305.1	n.230+35054T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102810 AN: 151962 Hom.: 40848 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.676 AC: 102816 AN: 152080 Hom.: 40853 Cov.: 32 AF XY: 0.681 AC XY: 50659 AN XY: 74366

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.729

Alfa AF: 0.756 Hom.: 5718

Bravo AF: 0.654

Asia WGS AF: 0.706 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs857440; hg19: chr6-14706177;