1-221443734-A-C

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372932	XR_922621.2	n.623-26408A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;