rs2073588

Positions:

• chr11-61968939-A-C

Variant summary

Our verdict is Benign. Variant got -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: ENST00000623785.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000623785.2	n.1211A>C		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.0522

Gnomad4 AMR exome AF: 0.0660

Gnomad4 ASJ exome AF: 0.0128

Gnomad4 EAS exome AF: 0.0796

Gnomad4 SAS exome AF: 0.0119

Gnomad4 FIN exome AF: 0.0947

Gnomad4 NFE exome AF: 0.0405

Gnomad4 OTH exome AF: 0.0429

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

Gnomad4 AFR AF: 0.0815

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0548

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0532 Hom.: 325

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2073588; hg19: chr11-61736411;