rs6924119

Variant names:

• chr6-14676739-C-T
• rs6924119
• ENST00000629853.3:n.314-14446G>A

Variant summary

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

The ENST00000689305.1(ENSG00000234261):​n.231-14446G>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 ENST00000689305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 0 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000689305.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234261	ENST00000629853.3	TSL:5	n.314-14446G>A		intron	N/A
	ENSG00000234261	ENST00000689305.1		n.231-14446G>A		intron	N/A
	ENSG00000234261	ENST00000729738.1		n.111-32670G>A		intron	N/A

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

African (AFR) AF: 0.337 AC: 13929 AN: 41382

American (AMR) AF: 0.0400 AC: 611 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00982 AC: 34 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5162

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4818

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10608

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00451 AC: 307 AN: 68004

Other (OTH) AF: 0.0723 AC: 153 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.68
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6924119;

hg19: chr6-14676970;