chr6-43828231-G-T

Variant names:

• chr6-43828231-G-T
• rs943072
• ENST00000637813.1:n.366-14280G>T

Variant summary

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

The ENST00000637813.1(ENSG00000283573):​n.366-14280G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,194 control chromosomes in the GnomAD database, including 53,702 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 0.84 (53702 hom., cov: 33)
• Consequence: ENSG00000283573 ENST00000637813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 31 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637813.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283573	ENST00000637813.1	TSL:4	n.366-14280G>T		intron	N/A
	ENSG00000283573	ENST00000719551.1		n.193-14280G>T		intron	N/A
	ENSG00000283573	ENST00000719553.1		n.401-1843G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.835 AC: 127018 AN: 152076 Hom.: 53657 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.835 AC: 127120 AN: 152194 Hom.: 53702 Cov.: 33 AF XY: 0.835 AC XY: 62109 AN XY: 74416

African (AFR) AF: 0.706 AC: 29308 AN: 41494

American (AMR) AF: 0.771 AC: 11792 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3001 AN: 3470

East Asian (EAS) AF: 0.864 AC: 4465 AN: 5168

South Asian (SAS) AF: 0.914 AC: 4413 AN: 4826

European-Finnish (FIN) AF: 0.888 AC: 9421 AN: 10614

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61891 AN: 68006

Other (OTH) AF: 0.826 AC: 1745 AN: 2112

Alfa AF: 0.888 Hom.: 200860

Bravo AF: 0.819

Asia WGS AF: 0.873 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.7
DANN	Benign	0.78
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs943072; hg19: chr6-43795968;