11-61092414-T-G

Variant names:

• chr11-61092414-T-G
• rs612415
• ENST00000794255.1:n.18A>C

Variant summary

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

The ENST00000794255.1(ENSG00000303405):​n.18A>C 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 0.417 in 151,968 control chromosomes in the GnomAD database, including 14,402 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 0.42 (14402 hom., cov: 32)
• Consequence: ENSG00000303405 ENST00000794255.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 5 publications found

Genes affected

ENSG00000303405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369325	NR_188502.1	n.-56A>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303405	ENST00000794255.1	n.18A>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000303405	ENST00000794256.1	n.18A>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000303405	ENST00000794257.1	n.15A>C		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63335 AN: 151850 Hom.: 14389 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.417 AC: 63378 AN: 151968 Hom.: 14402 Cov.: 32 AF XY: 0.430 AC XY: 31898 AN XY: 74260

African (AFR) AF: 0.342 AC: 14170 AN: 41430

American (AMR) AF: 0.507 AC: 7743 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1453 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4744 AN: 5140

South Asian (SAS) AF: 0.601 AC: 2898 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5682 AN: 10566

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25467 AN: 67950

Other (OTH) AF: 0.397 AC: 837 AN: 2108

Alfa AF: 0.375 Hom.: 4773

Bravo AF: 0.412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0060
DANN	Benign	0.61
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs612415; hg19: chr11-60859886;