XR_922214.3:n.1903+192G>A

Variant names:

• chr1-161493811-G-A
• rs7512140
• XR_922214.3:n.1903+192G>A

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,070 control chromosomes in the GnomAD database, including 25,061 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 0.57 (25061 hom., cov: 33)
• Consequence: LOC105371473 XR_922214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 9 publications found

Genes affected

LOC105371473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371473	XR_922214.3	n.1903+192G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86412 AN: 151952 Hom.: 25056 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.569 AC: 86469 AN: 152070 Hom.: 25061 Cov.: 33 AF XY: 0.565 AC XY: 41983 AN XY: 74334

African (AFR) AF: 0.543 AC: 22510 AN: 41472

American (AMR) AF: 0.604 AC: 9226 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1287 AN: 5184

South Asian (SAS) AF: 0.423 AC: 2035 AN: 4816

European-Finnish (FIN) AF: 0.584 AC: 6164 AN: 10558

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41549 AN: 67978

Other (OTH) AF: 0.564 AC: 1192 AN: 2114

Alfa AF: 0.582 Hom.: 4203

Bravo AF: 0.571

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.74
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7512140; hg19: chr1-161463601;