rs11168068

Variant names:

• chr5-148824558-C-T
• rs11168068
• ENST00000798472.1:n.254+398C>T

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.254+398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,608 control chromosomes in the GnomAD database, including 27,541 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 0.60 (27541 hom., cov: 31)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 8 publications found

Genes affected

ENSG00000303969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798472.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303969	ENST00000798472.1		n.254+398C>T		intron	N/A
	ENSG00000303969	ENST00000798473.1		n.251+398C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90636 AN: 151490 Hom.: 27522 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.598 AC: 90700 AN: 151608 Hom.: 27541 Cov.: 31 AF XY: 0.606 AC XY: 44888 AN XY: 74100

African (AFR) AF: 0.565 AC: 23267 AN: 41184

American (AMR) AF: 0.711 AC: 10853 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3468

East Asian (EAS) AF: 0.744 AC: 3849 AN: 5170

South Asian (SAS) AF: 0.741 AC: 3567 AN: 4812

European-Finnish (FIN) AF: 0.633 AC: 6622 AN: 10468

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38377 AN: 67930

Other (OTH) AF: 0.630 AC: 1329 AN: 2110

Alfa AF: 0.583 Hom.: 12752

Bravo AF: 0.599

Asia WGS AF: 0.747 AC: 2595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.0030

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11168068;

hg19: chr5-148204121;