rs1870874

Positions:

• chr11-40110654-A-C

Variant summary

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

The ENST00000624239.1(ENSG00000279675):​n.1946T>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 0.469 in 151,828 control chromosomes in the GnomAD database, including 17,969 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 0.47 (17969 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000624239.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000624239.1	n.1946T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71056 AN: 151710 Hom.: 17915 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.482

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.469 AC: 71174 AN: 151828 Hom.: 17969 Cov.: 32 AF XY: 0.463 AC XY: 34359 AN XY: 74222

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.485

Alfa AF: 0.432 Hom.: 2416

Bravo AF: 0.496

Asia WGS AF: 0.468 AC: 1620 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870874; hg19: chr11-40132204; COSMIC: COSV53419690;