chr12-114943935-G-A

Variant names:

• chr12-114943935-G-A
• rs10850409
• ENST00000768418.1:n.94+9821G>A

Variant summary

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

The ENST00000768418.1(ENSG00000300044):​n.94+9821G>A 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 152,056 control chromosomes in the GnomAD database, including 6,185 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 (6185 hom., cov: 32)
• Consequence: ENSG00000300044 ENST00000768418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 31 publications found

Genes affected

ENSG00000300044 (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 = 0.524 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
ENSG00000300044	ENST00000768418.1	n.94+9821G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41216 AN: 151934 Hom.: 6178 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.271 AC: 41252 AN: 152056 Hom.: 6185 Cov.: 32 AF XY: 0.279 AC XY: 20733 AN XY: 74330

African (AFR) AF: 0.221 AC: 9176 AN: 41470

American (AMR) AF: 0.411 AC: 6285 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2795 AN: 5166

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4816

European-Finnish (FIN) AF: 0.296 AC: 3133 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17444 AN: 67970

Other (OTH) AF: 0.268 AC: 565 AN: 2108

Alfa AF: 0.262 Hom.: 11103

Bravo AF: 0.279

Asia WGS AF: 0.368 AC: 1278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.29
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10850409; hg19: chr12-115381740;