1-147032846-T-C

Variant names:

• chr1-147032846-T-C
• rs12122534
• ENST00000444082.2:n.989-1708A>G

Variant summary

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

The ENST00000444082.2(ENSG00000227242):​n.989-1708A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,010 control chromosomes in the GnomAD database, including 32,064 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 0.65 (32064 hom., cov: 32)
• Consequence: ENSG00000227242 ENST00000444082.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 4 publications found

Genes affected

ENSG00000227242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC728989	NR_024442.2	n.91-7922A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227242	ENST00000444082.2	n.989-1708A>G		intron_variant	Intron 8 of 14	6
ENSG00000310005	ENST00000846524.1	n.389-1706A>G		intron_variant	Intron 1 of 7
ENSG00000310005	ENST00000846525.1	n.124-1706A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98033 AN: 151892 Hom.: 32021 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.646 AC: 98142 AN: 152010 Hom.: 32064 Cov.: 32 AF XY: 0.657 AC XY: 48820 AN XY: 74278

African (AFR) AF: 0.600 AC: 24867 AN: 41464

American (AMR) AF: 0.695 AC: 10612 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1954 AN: 3470

East Asian (EAS) AF: 0.864 AC: 4451 AN: 5150

South Asian (SAS) AF: 0.737 AC: 3556 AN: 4824

European-Finnish (FIN) AF: 0.751 AC: 7920 AN: 10548

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42537 AN: 67968

Other (OTH) AF: 0.640 AC: 1352 AN: 2114

Alfa AF: 0.600 Hom.: 3111

Bravo AF: 0.644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs12122534; hg19: chr1-146504399;