6-14705946-A-G

Variant names:

• chr6-14705946-A-G
• rs857440
• ENST00000629853.3:n.314-43653T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000629853.3(ENSG00000234261):​n.314-43653T>C variant causes a intron 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: ENSG00000234261 ENST00000629853.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 1 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629853.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234261	ENST00000629853.3	TSL:5	n.314-43653T>C		intron	N/A
	ENSG00000234261	ENST00000689305.1		n.230+35054T>C		intron	N/A
	ENSG00000234261	ENST00000729738.1		n.111-61877T>C		intron	N/A

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

African (AFR) AF: 0.224 AC: 9267 AN: 41462

American (AMR) AF: 0.830 AC: 12676 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2952 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3562 AN: 5170

South Asian (SAS) AF: 0.787 AC: 3801 AN: 4828

European-Finnish (FIN) AF: 0.868 AC: 9198 AN: 10592

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58734 AN: 67968

Other (OTH) AF: 0.729 AC: 1539 AN: 2110

Alfa AF: 0.735 Hom.: 5746

Bravo AF: 0.654

Asia WGS AF: 0.706 AC: 2455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs857440; hg19: chr6-14706177;