chr4-141377548-G-A

Variant names:

• chr4-141377548-G-A
• rs4267812
• ENST00000821082.1:n.213+43774G>A

Variant summary

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

The ENST00000821082.1(ENSG00000306779):​n.213+43774G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,152 control chromosomes in the GnomAD database, including 58,970 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 0.88 (58970 hom., cov: 31)
• Consequence: ENSG00000306779 ENST00000821082.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 4 publications found

Genes affected

ENSG00000306779 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 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
ENSG00000306779	ENST00000821082.1	n.213+43774G>A		intron_variant	Intron 1 of 1
ENSG00000306779	ENST00000821083.1	n.318-9556G>A		intron_variant	Intron 2 of 2
ENSG00000306779	ENST00000821084.1	n.200-9556G>A		intron_variant	Intron 1 of 1
ENSG00000306779	ENST00000821085.1	n.150-8664G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133377 AN: 152034 Hom.: 58915 Cov.: 31

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.877 AC: 133488 AN: 152152 Hom.: 58970 Cov.: 31 AF XY: 0.874 AC XY: 64974 AN XY: 74380

African (AFR) AF: 0.956 AC: 39683 AN: 41504

American (AMR) AF: 0.808 AC: 12366 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3124 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3030 AN: 5158

South Asian (SAS) AF: 0.880 AC: 4232 AN: 4808

European-Finnish (FIN) AF: 0.836 AC: 8851 AN: 10584

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59424 AN: 68008

Other (OTH) AF: 0.886 AC: 1871 AN: 2112

Alfa AF: 0.872 Hom.: 57451

Bravo AF: 0.872

Asia WGS AF: 0.790 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.45
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4267812; hg19: chr4-142298702;