chr12-6181927-G-A

Variant names:

• chr12-6181927-G-A
• rs7342306
• ENST00000810805.1:n.109+18609C>T

Variant summary

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

The ENST00000810805.1(ENSG00000255775):​n.109+18609C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,094 control chromosomes in the GnomAD database, including 9,038 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 0.33 (9038 hom., cov: 33)
• Consequence: ENSG00000255775 ENST00000810805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 26 publications found

Genes affected

ENSG00000255775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810805.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255775	ENST00000810805.1		n.109+18609C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50804 AN: 151976 Hom.: 9036 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.334 AC: 50832 AN: 152094 Hom.: 9038 Cov.: 33 AF XY: 0.328 AC XY: 24357 AN XY: 74324

African (AFR) AF: 0.238 AC: 9886 AN: 41520

American (AMR) AF: 0.259 AC: 3952 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1705 AN: 5140

South Asian (SAS) AF: 0.286 AC: 1379 AN: 4826

European-Finnish (FIN) AF: 0.373 AC: 3937 AN: 10568

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27914 AN: 67972

Other (OTH) AF: 0.306 AC: 645 AN: 2108

Alfa AF: 0.387 Hom.: 34535

Bravo AF: 0.321

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.53
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7342306; hg19: chr12-6291093;