chr12-107685408-G-A

Variant names:

• chr12-107685408-G-A
• rs744266
• ENST00000811485.1:n.257+75C>T

Variant summary

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

The ENST00000811485.1(ENSG00000305520):​n.257+75C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,744 control chromosomes in the GnomAD database, including 6,116 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 0.27 (6116 hom., cov: 31)
• Consequence: ENSG00000305520 ENST00000811485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 12 publications found

Genes affected

ENSG00000305520 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811485.1. 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
	ENSG00000305520	ENST00000811485.1		n.257+75C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41108 AN: 151626 Hom.: 6096 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.271 AC: 41169 AN: 151744 Hom.: 6116 Cov.: 31 AF XY: 0.279 AC XY: 20644 AN XY: 74118

African (AFR) AF: 0.195 AC: 8082 AN: 41366

American (AMR) AF: 0.339 AC: 5170 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 705 AN: 3464

East Asian (EAS) AF: 0.582 AC: 2998 AN: 5154

South Asian (SAS) AF: 0.326 AC: 1567 AN: 4814

European-Finnish (FIN) AF: 0.333 AC: 3466 AN: 10418

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18328 AN: 67952

Other (OTH) AF: 0.274 AC: 578 AN: 2108

Alfa AF: 0.269 Hom.: 3131

Bravo AF: 0.270

Asia WGS AF: 0.469 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		-0.82
PromoterAI		-0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs744266; hg19: chr12-108079185;