rs2971589

chr12-93991936-G-A

Variant summary

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

The XR_001749263.2(LOC105369912):n.161+4396C>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 0.163 in 152,196 control chromosomes in the GnomAD database, including 2,130 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 0.16 (2130 hom., cov: 32)
• Consequence: LOC105369912 XR_001749263.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

LOC105369912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369912	XR_001749263.2	n.161+4396C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24796 AN: 152078 Hom.: 2132 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.163 AC: 24789 AN: 152196 Hom.: 2130 Cov.: 32 AF XY: 0.159 AC XY: 11798 AN XY: 74422

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.179

Alfa AF: 0.181 Hom.: 3537

Bravo AF: 0.159

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2971589; hg19: chr12-94385712;