rs1150964

Variant names:

• chr12-31779355-C-A
• rs1150964
• XR_001749064.3:n.548-169G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-31779355-C-A
• chr12-31779355-C-G

Variant summary

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

The XR_001749064.3(LOC107984470):​n.548-169G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,934 control chromosomes in the GnomAD database, including 28,252 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 0.61 (28252 hom., cov: 31)
• Consequence: LOC107984470 XR_001749064.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 0 publications found

Genes affected

LOC107984470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.735 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: 0.607 AC: 92109 AN: 151816 Hom.: 28206 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.607 AC: 92214 AN: 151934 Hom.: 28252 Cov.: 31 AF XY: 0.613 AC XY: 45526 AN XY: 74236

African (AFR) AF: 0.673 AC: 27877 AN: 41448

American (AMR) AF: 0.590 AC: 8999 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2130 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3740 AN: 5160

South Asian (SAS) AF: 0.756 AC: 3642 AN: 4820

European-Finnish (FIN) AF: 0.607 AC: 6401 AN: 10550

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37399 AN: 67926

Other (OTH) AF: 0.626 AC: 1318 AN: 2106

Alfa AF: 0.589 Hom.: 15646

Bravo AF: 0.607

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.68
DANN	Benign	0.26
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs1150964; hg19: chr12-31932289;