rs1805742

Variant names:

• chr12-8913250-G-C
• rs1805742
• ENST00000631830.1:n.321+1706C>G

Variant summary

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

The ENST00000631830.1(ENSG00000282022):​n.321+1706C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,078 control chromosomes in the GnomAD database, including 3,812 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 0.22 (3812 hom., cov: 32)
• Consequence: ENSG00000282022 ENST00000631830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 2 publications found

Genes affected

ENSG00000282022 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631830.1. 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
	ENSG00000282022	ENST00000631830.1	TSL:3	n.321+1706C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33240 AN: 151960 Hom.: 3809 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.219 AC: 33250 AN: 152078 Hom.: 3812 Cov.: 32 AF XY: 0.217 AC XY: 16144 AN XY: 74344

African (AFR) AF: 0.241 AC: 10006 AN: 41434

American (AMR) AF: 0.193 AC: 2957 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1578 AN: 5174

South Asian (SAS) AF: 0.323 AC: 1558 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1738 AN: 10576

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13661 AN: 68006

Other (OTH) AF: 0.233 AC: 491 AN: 2108

Alfa AF: 0.206 Hom.: 419

Bravo AF: 0.219

Asia WGS AF: 0.303 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.52
PhyloP100		-0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1805742;

hg19: chr12-9065846;