rs739857

Variant names:

• chr12-47574503-A-C
• rs739857
• ENST00000799111.1:n.91-13998A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-47574503-A-C
• chr12-47574503-A-G
• chr12-47574503-A-T

Variant summary

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

The ENST00000799111.1(ENSG00000304045):​n.91-13998A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,136 control chromosomes in the GnomAD database, including 9,490 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 0.32 (9490 hom., cov: 32)
• Consequence: ENSG00000304045 ENST00000799111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 3 publications found

Genes affected

ENSG00000304045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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
ENSG00000304045	ENST00000799111.1	n.91-13998A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48883 AN: 152018 Hom.: 9489 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.321 AC: 48880 AN: 152136 Hom.: 9490 Cov.: 32 AF XY: 0.320 AC XY: 23839 AN XY: 74388

African (AFR) AF: 0.104 AC: 4341 AN: 41544

American (AMR) AF: 0.281 AC: 4288 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3464

East Asian (EAS) AF: 0.328 AC: 1697 AN: 5176

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4820

European-Finnish (FIN) AF: 0.434 AC: 4581 AN: 10566

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29852 AN: 67960

Other (OTH) AF: 0.331 AC: 699 AN: 2114

Alfa AF: 0.401 Hom.: 45322

Bravo AF: 0.299

Asia WGS AF: 0.294 AC: 1023 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.67
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs739857; hg19: chr12-47968286;