rs1870874

Variant names:

• chr11-40110654-A-C
• rs1870874
• ENST00000624239.1:n.1946T>G

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000279675 ENST00000624239.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

Genes affected

ENSG00000279675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624239.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279675	ENST00000624239.1	TSL:6	n.1946T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000306946	ENST00000822121.1		n.137+224A>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.655 AC: 27164 AN: 41446

American (AMR) AF: 0.437 AC: 6655 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3220 AN: 5160

South Asian (SAS) AF: 0.268 AC: 1294 AN: 4826

European-Finnish (FIN) AF: 0.299 AC: 3161 AN: 10566

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26364 AN: 67830

Other (OTH) AF: 0.485 AC: 1022 AN: 2108

Alfa AF: 0.438 Hom.: 2564

Bravo AF: 0.496

Asia WGS AF: 0.468 AC: 1620 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

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

Other links and lift over

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