rs11664521

Variant names:

• chr18-2831498-G-A
• rs11664521
• ENST00000581172.1:n.450+1118C>T

Variant summary

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

The ENST00000581172.1(ENSG00000266049):​n.450+1118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,710 control chromosomes in the GnomAD database, including 2,351 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 0.15 (2351 hom., cov: 31)
• Consequence: ENSG00000266049 ENST00000581172.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

Genes affected

ENSG00000266049 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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
ENSG00000266049	ENST00000581172.1	n.450+1118C>T		intron_variant	Intron 1 of 1	3
ENSG00000266049	ENST00000583546.1	n.308+1118C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22705 AN: 151592 Hom.: 2345 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.150 AC: 22730 AN: 151710 Hom.: 2351 Cov.: 31 AF XY: 0.150 AC XY: 11120 AN XY: 74178

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.149

Alfa AF: 0.115 Hom.: 2543

Bravo AF: 0.156

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
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: rs11664521; hg19: chr18-2831496;