chr4-126549748-T-C

Variant names:

• chr4-126549748-T-C
• rs6810452
• ENST00000661809.1:n.149-84606A>G

Variant summary

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

The ENST00000661809.1(ENSG00000286251):​n.149-84606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,824 control chromosomes in the GnomAD database, including 31,162 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 0.64 (31162 hom., cov: 32)
• Consequence: ENSG00000286251 ENST00000661809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 3 publications found

Genes affected

ENSG00000286251 (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 (SAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661809.1. 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
	ENSG00000286251	ENST00000661809.1		n.149-84606A>G		intron	N/A
	ENSG00000286251	ENST00000816599.1		n.128-13061A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96822 AN: 151706 Hom.: 31127 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.638 AC: 96909 AN: 151824 Hom.: 31162 Cov.: 32 AF XY: 0.635 AC XY: 47100 AN XY: 74186

African (AFR) AF: 0.652 AC: 27016 AN: 41410

American (AMR) AF: 0.532 AC: 8089 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2458 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2671 AN: 5132

South Asian (SAS) AF: 0.667 AC: 3219 AN: 4824

European-Finnish (FIN) AF: 0.649 AC: 6855 AN: 10564

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44518 AN: 67908

Other (OTH) AF: 0.644 AC: 1357 AN: 2108

Alfa AF: 0.647 Hom.: 17241

Bravo AF: 0.627

Asia WGS AF: 0.622 AC: 2161 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.65
PhyloP100		0.41

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: rs6810452;

hg19: chr4-127470903;