6-44457063-A-G

Variant names:

• chr6-44457063-A-G
• rs543844
• ENST00000793254.1:n.145A>G

Variant summary

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

The ENST00000793254.1(ENSG00000303259):​n.145A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,824 control chromosomes in the GnomAD database, including 22,399 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 0.51 (22399 hom., cov: 31)
• Consequence: ENSG00000303259 ENST00000793254.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 9 publications found

Genes affected

ENSG00000303259 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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
ENSG00000303259	ENST00000793254.1	n.145A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77606 AN: 151706 Hom.: 22363 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.512 AC: 77704 AN: 151824 Hom.: 22399 Cov.: 31 AF XY: 0.519 AC XY: 38520 AN XY: 74160

African (AFR) AF: 0.742 AC: 30700 AN: 41366

American (AMR) AF: 0.570 AC: 8689 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3466

East Asian (EAS) AF: 0.809 AC: 4172 AN: 5160

South Asian (SAS) AF: 0.631 AC: 3034 AN: 4810

European-Finnish (FIN) AF: 0.379 AC: 3988 AN: 10524

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23846 AN: 67938

Other (OTH) AF: 0.532 AC: 1122 AN: 2108

Alfa AF: 0.404 Hom.: 57293

Bravo AF: 0.537

Asia WGS AF: 0.726 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs543844; hg19: chr6-44424800;