rs2053949

Variant names:

• chr6-159603813-C-T
• rs2053949
• ENST00000656085.1:n.42+58773G>A

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+58773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,840 control chromosomes in the GnomAD database, including 20,785 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 0.50 (20785 hom., cov: 31)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 6 publications found

Genes affected

ENSG00000286533 (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 (AFR) allele frequency at 95% confidence interval = 0.727 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
ENSG00000286533	ENST00000656085.1	n.42+58773G>A		intron_variant	Intron 1 of 1
ENSG00000286533	ENST00000794978.1	n.186-8609G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75978 AN: 151722 Hom.: 20727 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.501 AC: 76088 AN: 151840 Hom.: 20785 Cov.: 31 AF XY: 0.498 AC XY: 36929 AN XY: 74176

African (AFR) AF: 0.734 AC: 30396 AN: 41406

American (AMR) AF: 0.371 AC: 5658 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3470

East Asian (EAS) AF: 0.579 AC: 2996 AN: 5172

South Asian (SAS) AF: 0.443 AC: 2132 AN: 4810

European-Finnish (FIN) AF: 0.377 AC: 3957 AN: 10490

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27971 AN: 67940

Other (OTH) AF: 0.467 AC: 984 AN: 2106

Alfa AF: 0.465 Hom.: 2964

Bravo AF: 0.511

Asia WGS AF: 0.521 AC: 1816 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	1.9
DANN	Benign	0.75
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2053949; hg19: chr6-160024845;