rs1150964

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001749064.3(LOC107984470):​n.548-169G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

LOC107984470 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984470	XR_001749064.3	n.548-169G>T		intron_variant, non_coding_transcript_variant
LOC107984470	XR_001749065.3	n.554-169G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.626

Alfa AF: 0.569 Hom.: 5138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150964; hg19: chr12-31932289;