6-14748444-T-C

Variant names:

• chr6-14748444-T-C
• rs2472793
• ENST00000629853.3:n.313+41546A>G

Variant summary

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

The ENST00000629853.3(ENSG00000234261):​n.313+41546A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,074 control chromosomes in the GnomAD database, including 52,646 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 0.82 (52646 hom., cov: 31)
• Consequence: ENSG00000234261 ENST00000629853.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 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.313+41546A>G		intron	N/A
	ENSG00000234261	ENST00000689305.1		n.179-7393A>G		intron	N/A
	ENSG00000234261	ENST00000702363.1		n.187-16966A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124797 AN: 151956 Hom.: 52634 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.821 AC: 124851 AN: 152074 Hom.: 52646 Cov.: 31 AF XY: 0.824 AC XY: 61261 AN XY: 74316

African (AFR) AF: 0.610 AC: 25286 AN: 41432

American (AMR) AF: 0.850 AC: 12980 AN: 15274

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

East Asian (EAS) AF: 0.949 AC: 4903 AN: 5166

South Asian (SAS) AF: 0.909 AC: 4381 AN: 4818

European-Finnish (FIN) AF: 0.912 AC: 9646 AN: 10580

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61564 AN: 68014

Other (OTH) AF: 0.845 AC: 1787 AN: 2114

Alfa AF: 0.877 Hom.: 228497

Bravo AF: 0.804

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.63
DANN	Benign	0.53
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2472793; hg19: chr6-14748675;