rs6581768

Positions:

• chr12-67683408-A-G

Variant summary

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

The XR_945051.3(LOC105369816):​n.10230A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,096 control chromosomes in the GnomAD database, including 5,377 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 0.25 (5377 hom., cov: 32)
• Consequence: LOC105369816 XR_945051.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

LOC105369816 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369816	XR_945051.3	n.10230A>G		non_coding_transcript_exon_variant	2/2
LOC105369816	XR_945052.3	n.10116A>G		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38366 AN: 151978 Hom.: 5379 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.252 AC: 38356 AN: 152096 Hom.: 5377 Cov.: 32 AF XY: 0.251 AC XY: 18676 AN XY: 74344

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.290

Alfa AF: 0.265 Hom.: 699

Bravo AF: 0.254

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6581768; hg19: chr12-68077188; COSMIC: COSV51093992;