rs12529874

Variant names:

• chr6-98014625-G-A
• rs12529874
• ENST00000606913.5:n.156-84561G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000606913.5(ENSG00000271860):​n.156-84561G>A variant causes a intron change. The variant allele was found at a frequency of 0.027 in 152,014 control chromosomes in the GnomAD database, including 74 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 0.027 (74 hom., cov: 32)
• Consequence: ENSG00000271860 ENST00000606913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.04
• Publications: 6 publications found

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.027 (4099/152014) while in subpopulation EAS AF = 0.0454 (233/5128). AF 95% confidence interval is 0.0407. There are 74 homozygotes in GnomAd4. There are 2051 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 74 gene

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
ENSG00000271860	ENST00000606913.5	n.156-84561G>A		intron_variant	Intron 1 of 4	5
ENSG00000271860	ENST00000607032.1	n.246+45159G>A		intron_variant	Intron 2 of 7	3
ENSG00000271860	ENST00000607823.5	n.267+45159G>A		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4092 AN: 151896 Hom.: 75 Cov.: 32

Gnomad AFR AF: 0.00740

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0290

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0270 AC: 4099 AN: 152014 Hom.: 74 Cov.: 32 AF XY: 0.0276 AC XY: 2051 AN XY: 74314

African (AFR) AF: 0.00737 AC: 306 AN: 41494

American (AMR) AF: 0.0289 AC: 441 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3472

East Asian (EAS) AF: 0.0454 AC: 233 AN: 5128

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4826

European-Finnish (FIN) AF: 0.0296 AC: 314 AN: 10616

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0330 AC: 2242 AN: 67920

Other (OTH) AF: 0.0413 AC: 87 AN: 2108

Alfa AF: 0.0278 Hom.: 65

Bravo AF: 0.0251

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	19
DANN	Benign	0.81
PhyloP100		5.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12529874; hg19: chr6-98462501;