rs6756739

Variant names:

• chr2-52957990-C-T
• rs6756739
• ENST00000421575.7:n.116+3379G>A

Variant summary

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

The NR_187747.1(LOC105369165):​n.49-47966G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,908 control chromosomes in the GnomAD database, including 22,607 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 (22607 hom., cov: 31)
• Consequence: LOC105369165 NR_187747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 6 publications found

Genes affected

ENSG00000228033 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187747.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105369165	NR_187747.1		n.49-47966G>A		intron	N/A
	LOC105369165	NR_187748.1		n.49-47966G>A		intron	N/A
	LOC105369165	NR_187750.1		n.49-47966G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228033	ENST00000421575.7	TSL:5	n.116+3379G>A		intron	N/A
	ENSG00000228033	ENST00000809539.1		n.116+3379G>A		intron	N/A
	ENSG00000228033	ENST00000809540.1		n.72+3379G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75838 AN: 151790 Hom.: 22556 Cov.: 31

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.500 AC: 75943 AN: 151908 Hom.: 22607 Cov.: 31 AF XY: 0.492 AC XY: 36511 AN XY: 74220

African (AFR) AF: 0.844 AC: 34953 AN: 41434

American (AMR) AF: 0.345 AC: 5275 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3468

East Asian (EAS) AF: 0.0525 AC: 271 AN: 5160

South Asian (SAS) AF: 0.444 AC: 2129 AN: 4796

European-Finnish (FIN) AF: 0.380 AC: 3995 AN: 10526

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26595 AN: 67930

Other (OTH) AF: 0.452 AC: 953 AN: 2108

Alfa AF: 0.443 Hom.: 15170

Bravo AF: 0.507

Asia WGS AF: 0.319 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.66
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs6756739; hg19: chr2-53185128;