6-14737278-A-G

Variant names:

• chr6-14737278-A-G
• rs2038016
• ENST00000629853.3:n.313+52712T>C

Variant summary

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

The ENST00000689305.1(ENSG00000234261):​n.230+3722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,204 control chromosomes in the GnomAD database, including 56,174 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 0.85 (56174 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000689305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234261	ENST00000629853.3	n.313+52712T>C		intron_variant	Intron 3 of 3	5
ENSG00000234261	ENST00000689305.1	n.230+3722T>C		intron_variant	Intron 2 of 2
ENSG00000234261	ENST00000702363.1	n.187-5800T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.855 AC: 130017 AN: 152086 Hom.: 56143 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.855 AC: 130100 AN: 152204 Hom.: 56174 Cov.: 32 AF XY: 0.857 AC XY: 63785 AN XY: 74422

African (AFR) AF: 0.725 AC: 30094 AN: 41494

American (AMR) AF: 0.864 AC: 13210 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3262 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5014 AN: 5172

South Asian (SAS) AF: 0.910 AC: 4397 AN: 4832

European-Finnish (FIN) AF: 0.911 AC: 9668 AN: 10610

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61586 AN: 68012

Other (OTH) AF: 0.863 AC: 1825 AN: 2114

Alfa AF: 0.889 Hom.: 99148

Bravo AF: 0.842

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.37
PhyloP100		-0.32

Splicing

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

Publications

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Other links and lift over

dbSNP: rs2038016; hg19: chr6-14737509;