rs10850408

Variant names:

• chr12-114942588-C-T
• rs10850408
• ENST00000768418.1:n.94+8474C>T

Variant summary

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

The ENST00000768418.1(ENSG00000300044):​n.94+8474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,036 control chromosomes in the GnomAD database, including 7,703 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 0.31 (7703 hom., cov: 32)
• Consequence: ENSG00000300044 ENST00000768418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 9 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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+8474C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47334 AN: 151920 Hom.: 7694 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.312 AC: 47372 AN: 152036 Hom.: 7703 Cov.: 32 AF XY: 0.307 AC XY: 22821 AN XY: 74320

African (AFR) AF: 0.338 AC: 13990 AN: 41438

American (AMR) AF: 0.261 AC: 3987 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3464

East Asian (EAS) AF: 0.142 AC: 737 AN: 5180

South Asian (SAS) AF: 0.431 AC: 2079 AN: 4826

European-Finnish (FIN) AF: 0.226 AC: 2392 AN: 10572

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21733 AN: 67976

Other (OTH) AF: 0.329 AC: 694 AN: 2110

Alfa AF: 0.326 Hom.: 18850

Bravo AF: 0.313

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.69
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10850408; hg19: chr12-115380393;