chr12-31779355-C-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984470	XR_001749064.3	n.548-169G>T		intron_variant	Intron 2 of 2
LOC107984470	XR_001749065.3	n.554-169G>T		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;