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 ENST00000629853.3(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 ENST00000629853.3 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928354	XR_001743992.2	n.47-32670G>A		intron_variant	Intron 1 of 4
LOC101928354	XR_241980.4	n.47-32670G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234261	ENST00000629853.3	n.314-14446G>A		intron_variant	Intron 3 of 3	5
ENSG00000234261	ENST00000689305.1	n.231-14446G>A		intron_variant	Intron 2 of 2
ENSG00000234261	ENST00000729738.1	n.111-32670G>A		intron_variant	Intron 1 of 7

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 v4.3

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

Other links and lift over

dbSNP: rs6924119; hg19: chr6-14676970;