chr11-4495346-C-T

Variant names:

• chr11-4495346-C-T
• rs10160399
• ENST00000685350.2:n.569-24317C>T

Variant summary

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

The ENST00000685350.2(ENSG00000291144):​n.569-24317C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,142 control chromosomes in the GnomAD database, including 1,161 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 0.10 (1161 hom., cov: 32)
• Consequence: ENSG00000291144 ENST00000685350.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 5 publications found

Genes affected

ENSG00000291144 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685350.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291144	ENST00000685350.2		n.569-24317C>T		intron	N/A
	ENSG00000291144	ENST00000690302.2		n.399-24317C>T		intron	N/A
	ENSG00000291144	ENST00000691418.2		n.374-23401C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15659 AN: 152024 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.103 AC: 15718 AN: 152142 Hom.: 1161 Cov.: 32 AF XY: 0.101 AC XY: 7524 AN XY: 74370

African (AFR) AF: 0.209 AC: 8666 AN: 41466

American (AMR) AF: 0.0664 AC: 1014 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3472

East Asian (EAS) AF: 0.0875 AC: 452 AN: 5168

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4830

European-Finnish (FIN) AF: 0.0417 AC: 443 AN: 10612

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4280 AN: 68000

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.0805 Hom.: 1865

Bravo AF: 0.113

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.23
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10160399; hg19: chr11-4516576;