rs1997111

Variant names:

• chr12-118950113-A-C
• rs1997111
• XR_945428.4:n.290-3249T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-118950113-A-C
• chr12-118950113-A-G
• chr12-118950113-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_945428.4(LOC105370020):​n.290-3249T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,984 control chromosomes in the GnomAD database, including 32,615 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 0.65 (32615 hom., cov: 32)
• Consequence: LOC105370020 XR_945428.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.987
• Publications: 17 publications found

Genes affected

LOC105370020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99326 AN: 151866 Hom.: 32566 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.654 AC: 99438 AN: 151984 Hom.: 32615 Cov.: 32 AF XY: 0.652 AC XY: 48455 AN XY: 74276

African (AFR) AF: 0.643 AC: 26628 AN: 41442

American (AMR) AF: 0.707 AC: 10782 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2860 AN: 5160

South Asian (SAS) AF: 0.500 AC: 2401 AN: 4806

European-Finnish (FIN) AF: 0.685 AC: 7238 AN: 10568

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44620 AN: 67964

Other (OTH) AF: 0.692 AC: 1461 AN: 2110

Alfa AF: 0.654 Hom.: 137127

Bravo AF: 0.662

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs1997111; hg19: chr12-119387918;