rs12032381

Positions:

• chr1-221443734-A-C

Variant summary

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

The XR_922621.2(LOC105372932):​n.623-26408A>C 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 0.193 in 151,822 control chromosomes in the GnomAD database, including 3,368 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 0.19 (3368 hom., cov: 32)
• Consequence: LOC105372932 XR_922621.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

LOC105372932 (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 (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372932	XR_922621.2	n.623-26408A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29331 AN: 151704 Hom.: 3366 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.193 AC: 29339 AN: 151822 Hom.: 3368 Cov.: 32 AF XY: 0.198 AC XY: 14697 AN XY: 74178

Gnomad4 AFR AF: 0.0622

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.203

Alfa AF: 0.226 Hom.: 1688

Bravo AF: 0.185

Asia WGS AF: 0.289 AC: 1004 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	0.38
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12032381; hg19: chr1-221617076;