rs701078

Variant names:

• chr12-124659907-C-T
• rs701078
• ENST00000767262.1:n.308+8143G>A

Variant summary

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

The ENST00000767262.1(ENSG00000299894):​n.308+8143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,186 control chromosomes in the GnomAD database, including 2,652 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 0.17 (2652 hom., cov: 32)
• Consequence: ENSG00000299894 ENST00000767262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 4 publications found

Genes affected

ENSG00000299894 (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 (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299894	ENST00000767262.1	n.308+8143G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26082 AN: 152068 Hom.: 2642 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.172 AC: 26126 AN: 152186 Hom.: 2652 Cov.: 32 AF XY: 0.176 AC XY: 13083 AN XY: 74416

African (AFR) AF: 0.270 AC: 11207 AN: 41504

American (AMR) AF: 0.150 AC: 2300 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.00366 AC: 19 AN: 5188

South Asian (SAS) AF: 0.124 AC: 596 AN: 4820

European-Finnish (FIN) AF: 0.225 AC: 2382 AN: 10592

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

European-Non Finnish (NFE) AF: 0.129 AC: 8760 AN: 68004

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.138 Hom.: 2701

Bravo AF: 0.172

Asia WGS AF: 0.0840 AC: 291 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	2.3
DANN	Benign	0.74
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs701078; hg19: chr12-125144453;