rs12195350

Variant names:

• chr6-43397622-A-G
• rs12195350
• ENST00000657856.1:n.579A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657856.1(ENSG00000287055):​n.579A>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 0.245 in 151,768 control chromosomes in the GnomAD database, including 4,766 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 0.24 (4766 hom., cov: 30)
• Consequence: ENSG00000287055 ENST00000657856.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 7 publications found

Genes affected

ENSG00000287055 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375065	XR_001744123.2	n.648A>G		non_coding_transcript_exon_variant	Exon 2 of 5
LOC105375065	XR_001744124.2	n.648A>G		non_coding_transcript_exon_variant	Exon 2 of 3
LOC105375065	XR_002956348.2	n.648A>G		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287055	ENST00000657856.1	n.579A>G		non_coding_transcript_exon_variant	Exon 2 of 6

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37108 AN: 151650 Hom.: 4755 Cov.: 30

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.245 AC: 37144 AN: 151768 Hom.: 4766 Cov.: 30 AF XY: 0.242 AC XY: 17937 AN XY: 74158

African (AFR) AF: 0.322 AC: 13325 AN: 41328

American (AMR) AF: 0.204 AC: 3109 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 855 AN: 3462

East Asian (EAS) AF: 0.277 AC: 1428 AN: 5150

South Asian (SAS) AF: 0.272 AC: 1305 AN: 4792

European-Finnish (FIN) AF: 0.171 AC: 1801 AN: 10546

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14563 AN: 67942

Other (OTH) AF: 0.244 AC: 513 AN: 2104

Alfa AF: 0.229 Hom.: 11934

Bravo AF: 0.249

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs12195350; hg19: chr6-43365360;