12-71053009-T-C

Variant names:

• chr12-71053009-T-C
• rs4760786
• ENST00000549357.2:n.610-5330A>G

Variant summary

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

The ENST00000549357.2(ENSG00000258053):​n.610-5330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,166 control chromosomes in the GnomAD database, including 5,035 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 0.23 (5035 hom., cov: 32)
• Consequence: ENSG00000258053 ENST00000549357.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 6 publications found

Genes affected

ENSG00000258053 (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 (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549357.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258053	ENST00000549357.2	TSL:1	n.610-5330A>G		intron	N/A
	ENSG00000258053	ENST00000716229.1		n.354-6268A>G		intron	N/A
	ENSG00000258053	ENST00000733252.1		n.356-5330A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34343 AN: 152048 Hom.: 5034 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.226 AC: 34348 AN: 152166 Hom.: 5035 Cov.: 32 AF XY: 0.222 AC XY: 16488 AN XY: 74384

African (AFR) AF: 0.0784 AC: 3257 AN: 41538

American (AMR) AF: 0.193 AC: 2951 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.00792 AC: 41 AN: 5174

South Asian (SAS) AF: 0.170 AC: 819 AN: 4826

European-Finnish (FIN) AF: 0.318 AC: 3367 AN: 10572

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22626 AN: 67978

Other (OTH) AF: 0.209 AC: 443 AN: 2116

Alfa AF: 0.276 Hom.: 11648

Bravo AF: 0.206

Asia WGS AF: 0.0850 AC: 296 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	1.2
DANN	Benign	0.85
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4760786; hg19: chr12-71446789;