rs2367446

Positions:

• chr12-76004953-T-C

Variant summary

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

The XR_945110.4(LOC105369847):​n.402+1236A>G 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 0.277 in 152,108 control chromosomes in the GnomAD database, including 6,793 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 0.28 (6793 hom., cov: 32)
• Consequence: LOC105369847 XR_945110.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

LOC105369847 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369847	XR_945110.4	n.402+1236A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42081 AN: 151990 Hom.: 6795 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.277 AC: 42061 AN: 152108 Hom.: 6793 Cov.: 32 AF XY: 0.282 AC XY: 20985 AN XY: 74342

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.259

Alfa AF: 0.316 Hom.: 4762

Bravo AF: 0.260

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.031
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2367446; hg19: chr12-76398733;