rs12032381

Variant names:

• chr1-221443734-A-C
• rs12032381
• XR_922621.2:n.623-26408A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-221443734-A-C
• chr1-221443734-A-G

Variant summary

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

The XR_922621.2(LOC105372932):​n.623-26408A>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 5 publications found

Genes affected

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

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0622 AC: 2578 AN: 41446

American (AMR) AF: 0.241 AC: 3669 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3458

East Asian (EAS) AF: 0.346 AC: 1789 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4808

European-Finnish (FIN) AF: 0.284 AC: 2993 AN: 10526

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15887 AN: 67876

Other (OTH) AF: 0.203 AC: 427 AN: 2102

Alfa AF: 0.221 Hom.: 3902

Bravo AF: 0.185

Asia WGS AF: 0.289 AC: 1004 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	0.38
DANN	Benign	0.21
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12032381; hg19: chr1-221617076;