chr4-157630147-C-T

Variant names:

• chr4-157630147-C-T
• rs6833943
• ENST00000652341.2:n.562+47080G>A

Variant summary

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

The ENST00000652341.2(ENSG00000287226):​n.562+47080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,970 control chromosomes in the GnomAD database, including 18,891 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 0.46 (18891 hom., cov: 32)
• Consequence: ENSG00000287226 ENST00000652341.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 3 publications found

Genes affected

ENSG00000287226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652341.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287226	ENST00000652341.2		n.562+47080G>A		intron	N/A
	ENSG00000287226	ENST00000809876.1		n.108-21909G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69224 AN: 151852 Hom.: 18886 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.456 AC: 69230 AN: 151970 Hom.: 18891 Cov.: 32 AF XY: 0.467 AC XY: 34654 AN XY: 74276

African (AFR) AF: 0.145 AC: 6000 AN: 41472

American (AMR) AF: 0.613 AC: 9359 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1419 AN: 3464

East Asian (EAS) AF: 0.801 AC: 4144 AN: 5174

South Asian (SAS) AF: 0.510 AC: 2459 AN: 4818

European-Finnish (FIN) AF: 0.638 AC: 6727 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37382 AN: 67904

Other (OTH) AF: 0.496 AC: 1048 AN: 2112

Alfa AF: 0.502 Hom.: 3719

Bravo AF: 0.445

Asia WGS AF: 0.614 AC: 2135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.56
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs6833943; hg19: chr4-158551299;