12-121131831-T-C

Variant names:

• chr12-121131831-T-C
• rs670541
• XR_001749352.3:n.328-4990A>G

Variant summary

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

The XR_001749352.3(LOC105370032):​n.328-4990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,174 control chromosomes in the GnomAD database, including 57,336 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 0.86 (57336 hom., cov: 31)
• Consequence: LOC105370032 XR_001749352.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 4 publications found

Genes affected

LOC105370032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370032	XR_001749352.3	n.328-4990A>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130992 AN: 152056 Hom.: 57306 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.861 AC: 131076 AN: 152174 Hom.: 57336 Cov.: 31 AF XY: 0.865 AC XY: 64319 AN XY: 74396

African (AFR) AF: 0.689 AC: 28578 AN: 41464

American (AMR) AF: 0.900 AC: 13761 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3318 AN: 3472

East Asian (EAS) AF: 0.941 AC: 4876 AN: 5182

South Asian (SAS) AF: 0.911 AC: 4391 AN: 4822

European-Finnish (FIN) AF: 0.935 AC: 9917 AN: 10604

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63283 AN: 68016

Other (OTH) AF: 0.880 AC: 1860 AN: 2114

Alfa AF: 0.859 Hom.: 9640

Bravo AF: 0.850

Asia WGS AF: 0.917 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.86
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs670541; hg19: chr12-121569634;