rs11650494

Positions:

• chr17-49267824-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655089.1(FLJ40194):​n.495+15150G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

FLJ40194 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLJ40194	ENST00000655089.1	n.495+15150G>A		intron_variant, non_coding_transcript_variant
FLJ40194	ENST00000656738.1	n.690+15150G>A		intron_variant, non_coding_transcript_variant
FLJ40194	ENST00000659323.1	n.882+14906G>A		intron_variant, non_coding_transcript_variant
FLJ40194	ENST00000663036.1	n.560+14906G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.00772

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.0772

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0946 Hom.: 255

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11650494; hg19: chr17-47345186;