16-23050918-C-T

Variant names:

• chr16-23050918-C-T
• rs10492791
• ENST00000719632.1:n.401-7353C>T

Variant summary

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

The ENST00000719632.1(ENSG00000261090):​n.401-7353C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 151,944 control chromosomes in the GnomAD database, including 38,994 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 0.71 (38994 hom., cov: 31)
• Consequence: ENSG00000261090 ENST00000719632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 5 publications found

Genes affected

ENSG00000261090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 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
ENSG00000261090	ENST00000719632.1	n.401-7353C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107879 AN: 151826 Hom.: 38980 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.710 AC: 107931 AN: 151944 Hom.: 38994 Cov.: 31 AF XY: 0.707 AC XY: 52507 AN XY: 74274

African (AFR) AF: 0.831 AC: 34469 AN: 41478

American (AMR) AF: 0.531 AC: 8100 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2448 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4028 AN: 5136

South Asian (SAS) AF: 0.737 AC: 3545 AN: 4812

European-Finnish (FIN) AF: 0.640 AC: 6770 AN: 10578

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46267 AN: 67904

Other (OTH) AF: 0.701 AC: 1477 AN: 2106

Alfa AF: 0.673 Hom.: 15514

Bravo AF: 0.705

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.68
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs10492791; hg19: chr16-23062239;