rs12499585

Variant names:

• chr4-40690870-C-T
• rs12499585
• ENST00000808992.1:n.557G>A

Variant summary

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

The ENST00000808992.1(ENSG00000305129):​n.557G>A 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 0.12 in 152,184 control chromosomes in the GnomAD database, including 1,852 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 0.12 (1852 hom., cov: 32)
• Consequence: ENSG00000305129 ENST00000808992.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 4 publications found

Genes affected

ENSG00000305129 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 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
ENSG00000305129	ENST00000808992.1	n.557G>A		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000305147	ENST00000809060.1	n.133C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18176 AN: 152066 Hom.: 1834 Cov.: 32

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.120 AC: 18206 AN: 152184 Hom.: 1852 Cov.: 32 AF XY: 0.129 AC XY: 9585 AN XY: 74394

African (AFR) AF: 0.0319 AC: 1324 AN: 41558

American (AMR) AF: 0.314 AC: 4787 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1647 AN: 5170

South Asian (SAS) AF: 0.262 AC: 1261 AN: 4814

European-Finnish (FIN) AF: 0.130 AC: 1378 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7118 AN: 68004

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.114 Hom.: 1649

Bravo AF: 0.130

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.57
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs12499585; hg19: chr4-40692887;