rs2712001

Variant names:

• chr4-39145429-T-C
• rs2712001
• ENST00000654813.2:n.357-4518A>G

Variant summary

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

The ENST00000654813.2(ENSG00000249207):​n.357-4518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,146 control chromosomes in the GnomAD database, including 44,701 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 0.76 (44701 hom., cov: 31)
• Consequence: ENSG00000249207 ENST00000654813.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 6 publications found

Genes affected

ENSG00000249207 (HGNC:58761):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654813.2. 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
	ENSG00000249207	ENST00000654813.2		n.357-4518A>G		intron	N/A
	ENSG00000249207	ENST00000668468.2		n.289+32189A>G		intron	N/A
	ENSG00000249207	ENST00000772109.1		n.345+32189A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115556 AN: 152028 Hom.: 44669 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.760 AC: 115634 AN: 152146 Hom.: 44701 Cov.: 31 AF XY: 0.763 AC XY: 56745 AN XY: 74372

African (AFR) AF: 0.613 AC: 25424 AN: 41474

American (AMR) AF: 0.823 AC: 12593 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2714 AN: 3470

East Asian (EAS) AF: 0.662 AC: 3427 AN: 5174

South Asian (SAS) AF: 0.834 AC: 4022 AN: 4820

European-Finnish (FIN) AF: 0.822 AC: 8710 AN: 10596

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56074 AN: 68000

Other (OTH) AF: 0.767 AC: 1619 AN: 2112

Alfa AF: 0.810 Hom.: 45688

Bravo AF: 0.753

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.60
PhyloP100		-0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2712001;

hg19: chr4-39147049;