chr12-275626-G-A

Variant names:

• chr12-275626-G-A
• rs525381
• ENST00000570140.1:n.1498C>T

Variant summary

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

The ENST00000703815.1(ENSG00000290285):​n.623G>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 0.314 in 151,978 control chromosomes in the GnomAD database, including 8,497 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 0.31 (8497 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: ENSG00000290285 ENST00000703815.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 7 publications found

Genes affected

ENSG00000261799 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703815.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261799	ENST00000570140.1	TSL:6	n.1498C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000290285	ENST00000703815.1		n.623G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47695 AN: 151850 Hom.: 8479 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.272

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.314 AC: 47750 AN: 151968 Hom.: 8497 Cov.: 32 AF XY: 0.313 AC XY: 23283 AN XY: 74274

African (AFR) AF: 0.490 AC: 20277 AN: 41422

American (AMR) AF: 0.208 AC: 3185 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 695 AN: 3466

East Asian (EAS) AF: 0.221 AC: 1144 AN: 5170

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4822

European-Finnish (FIN) AF: 0.318 AC: 3349 AN: 10542

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16816 AN: 67952

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.260 Hom.: 7276

Bravo AF: 0.314

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.34
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs525381; hg19: chr12-384792;