rs2073588

Variant names:

• chr11-61968939-A-C
• rs2073588
• ENST00000623785.2:n.1211A>C

Variant summary

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

The ENST00000623785.2(ENSG00000279491):​n.1211A>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 0.0648 in 175,288 control chromosomes in the GnomAD database, including 468 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 0.069 (435 hom., cov: 32)
  • Exomes 𝑓: 0.040 (33 hom.)
• Consequence: ENSG00000279491 ENST00000623785.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 10 publications found

Genes affected

ENSG00000279491 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC399900	NR_187560.1	n.*60A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279491	ENST00000623785.2	n.1211A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000303760	ENST00000797020.1	n.693T>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000303760	ENST00000797021.1	n.674T>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10428 AN: 152156 Hom.: 434 Cov.: 32

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0547

Gnomad OTH AF: 0.0511

GnomAD4 exome AF: 0.0397 AC: 913 AN: 23014 Hom.: 33 Cov.: 0 AF XY: 0.0376 AC XY: 465 AN XY: 12368

African (AFR) AF: 0.0522 AC: 7 AN: 134

American (AMR) AF: 0.0660 AC: 138 AN: 2092

Ashkenazi Jewish (ASJ) AF: 0.0128 AC: 4 AN: 312

East Asian (EAS) AF: 0.0796 AC: 43 AN: 540

South Asian (SAS) AF: 0.0119 AC: 57 AN: 4770

European-Finnish (FIN) AF: 0.0947 AC: 86 AN: 908

Middle Eastern (MID) AF: 0.0161 AC: 1 AN: 62

European-Non Finnish (NFE) AF: 0.0405 AC: 531 AN: 13124

Other (OTH) AF: 0.0429 AC: 46 AN: 1072

GnomAD4 genome AF: 0.0686 AC: 10439 AN: 152274 Hom.: 435 Cov.: 32 AF XY: 0.0716 AC XY: 5331 AN XY: 74454

African (AFR) AF: 0.0815 AC: 3387 AN: 41556

American (AMR) AF: 0.0619 AC: 946 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3468

East Asian (EAS) AF: 0.138 AC: 716 AN: 5186

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4828

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10598

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0548 AC: 3725 AN: 68024

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0561 Hom.: 534

Bravo AF: 0.0652

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.51
PhyloP100		0.091

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2073588; hg19: chr11-61736411;