11-61976870-C-T

Variant names:

• chr11-61976870-C-T
• rs195445
• ENST00000796889.1:n.184+9349C>T

Variant summary

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

The ENST00000796889.1(ENSG00000303745):​n.184+9349C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 151,988 control chromosomes in the GnomAD database, including 38,438 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 (38438 hom., cov: 30)
• Consequence: ENSG00000303745 ENST00000796889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 8 publications found

Genes affected

ENSG00000303745 (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 = 0.87 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
ENSG00000303745	ENST00000796889.1	n.184+9349C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107436 AN: 151870 Hom.: 38397 Cov.: 30

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.708 AC: 107536 AN: 151988 Hom.: 38438 Cov.: 30 AF XY: 0.713 AC XY: 52979 AN XY: 74272

African (AFR) AF: 0.682 AC: 28267 AN: 41456

American (AMR) AF: 0.815 AC: 12452 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2320 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4584 AN: 5140

South Asian (SAS) AF: 0.789 AC: 3801 AN: 4820

European-Finnish (FIN) AF: 0.670 AC: 7086 AN: 10574

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.685 AC: 46535 AN: 67940

Other (OTH) AF: 0.726 AC: 1532 AN: 2110

Alfa AF: 0.699 Hom.: 61532

Bravo AF: 0.714

Asia WGS AF: 0.846 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.73
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs195445; hg19: chr11-61744342;