rs1805742

Positions:

• chr12-8913250-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000631830.1(ENSG00000282022):​n.321+1706C>G variant causes a intron, non coding transcript 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: ENST00000631830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000631830.1	n.321+1706C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.233

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1805742; hg19: chr12-9065846;