rs174541

Positions:

• chr11-61798436-T-C

Variant summary

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

The ENST00000689245.1(ENSG00000289268):​n.710A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,164 control chromosomes in the GnomAD database, including 8,709 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 0.30 (8709 hom., cov: 31)
• Consequence: ENSG00000289268 ENST00000689245.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

ENSG00000289268 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.61798436T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289268	ENST00000689245.1	n.710A>G		non_coding_transcript_exon_variant	1/1
FADS2	ENST00000574708.5	n.49+5408T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45224 AN: 152044 Hom.: 8687 Cov.: 31

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.297 AC: 45257 AN: 152164 Hom.: 8709 Cov.: 31 AF XY: 0.304 AC XY: 22625 AN XY: 74402

Gnomad4 AFR AF: 0.0805

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.345

Alfa AF: 0.315 Hom.: 1090

Bravo AF: 0.297

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174541; hg19: chr11-61565908;