rs11650494

Variant names:

• chr17-49267824-G-A
• rs11650494
• ENST00000655089.1:n.495+15150G>A

Variant summary

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

The ENST00000655089.1(FLJ40194):​n.495+15150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,112 control chromosomes in the GnomAD database, including 1,500 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 0.12 (1500 hom., cov: 31)
• Consequence: FLJ40194 ENST00000655089.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 55 publications found

Genes affected

FLJ40194 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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
FLJ40194	ENST00000655089.1	n.495+15150G>A		intron_variant	Intron 2 of 5
FLJ40194	ENST00000656738.1	n.690+15150G>A		intron_variant	Intron 3 of 3
FLJ40194	ENST00000659323.1	n.882+14906G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17680 AN: 151994 Hom.: 1497 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00790

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.116 AC: 17696 AN: 152112 Hom.: 1500 Cov.: 31 AF XY: 0.111 AC XY: 8277 AN XY: 74360

African (AFR) AF: 0.232 AC: 9636 AN: 41462

American (AMR) AF: 0.0775 AC: 1184 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 557 AN: 3472

East Asian (EAS) AF: 0.00772 AC: 40 AN: 5178

South Asian (SAS) AF: 0.101 AC: 489 AN: 4820

European-Finnish (FIN) AF: 0.0215 AC: 228 AN: 10598

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0772 AC: 5246 AN: 67992

Other (OTH) AF: 0.114 AC: 242 AN: 2116

Alfa AF: 0.0949 Hom.: 1834

Bravo AF: 0.125

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.31
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs11650494; hg19: chr17-47345186;