2-624034-G-C

Variant names:

• chr2-624034-G-C
• rs6711012
• ENST00000846137.1:n.*60C>G

Variant summary

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

The ENST00000846137.1(ENSG00000309949):​n.*60C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,136 control chromosomes in the GnomAD database, including 55,129 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 0.85 (55129 hom., cov: 32)
• Consequence: ENSG00000309949 ENST00000846137.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 26 publications found

Genes affected

ENSG00000309949 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309949	ENST00000846137.1	n.*60C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129298 AN: 152018 Hom.: 55084 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.851 AC: 129399 AN: 152136 Hom.: 55129 Cov.: 32 AF XY: 0.852 AC XY: 63352 AN XY: 74364

African (AFR) AF: 0.887 AC: 36809 AN: 41506

American (AMR) AF: 0.872 AC: 13335 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2582 AN: 3464

East Asian (EAS) AF: 0.919 AC: 4754 AN: 5172

South Asian (SAS) AF: 0.802 AC: 3860 AN: 4810

European-Finnish (FIN) AF: 0.849 AC: 8975 AN: 10574

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56303 AN: 68004

Other (OTH) AF: 0.847 AC: 1788 AN: 2112

Alfa AF: 0.838 Hom.: 6230

Bravo AF: 0.854

Asia WGS AF: 0.871 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6711012; hg19: chr2-624034;