rs6581768

Variant names:

• chr12-67683408-A-G
• rs6581768
• XR_945051.3:n.10230A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LOC105369816 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105369816	XR_945051.3	n.10230A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105369816	XR_945052.3	n.10116A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.122 AC: 5069 AN: 41522

American (AMR) AF: 0.300 AC: 4582 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1809 AN: 5160

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4812

European-Finnish (FIN) AF: 0.196 AC: 2072 AN: 10584

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21007 AN: 67954

Other (OTH) AF: 0.290 AC: 613 AN: 2112

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
PhyloP100		1.1

Splicing

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

Other links and lift over

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