chr12-76642272-T-G

Position:

• chr12-76642272-T-G

Variant summary

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

The XR_945115.3(LOC105369851):​n.172-5623A>C 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 0.107 in 152,260 control chromosomes in the GnomAD database, including 1,236 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 0.11 (1236 hom., cov: 32)
• Consequence: LOC105369851 XR_945115.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

Genes affected

LOC105369851 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369851	XR_945115.3	n.172-5623A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16325 AN: 152142 Hom.: 1232 Cov.: 32

Gnomad AFR AF: 0.0318

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.107 AC: 16340 AN: 152260 Hom.: 1236 Cov.: 32 AF XY: 0.113 AC XY: 8377 AN XY: 74446

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.119

Alfa AF: 0.109 Hom.: 112

Bravo AF: 0.0985

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11114818; hg19: chr12-77036052;