chr6-50628740-G-A

Variant names:

• chr6-50628740-G-A
• rs1161397
• ENST00000431394.5:n.104+8022C>T

Variant summary

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

The ENST00000431394.5(ENSG00000230472):​n.104+8022C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 150,924 control chromosomes in the GnomAD database, including 5,068 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 0.21 (5068 hom., cov: 31)
• Consequence: ENSG00000230472 ENST00000431394.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• Publications: 4 publications found

Genes affected

ENSG00000230472 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.453 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
ENSG00000230472	ENST00000431394.5	n.104+8022C>T		intron_variant	Intron 1 of 4	3
ENSG00000230472	ENST00000454135.1	n.179+8022C>T		intron_variant	Intron 2 of 3	2
ENSG00000230472	ENST00000750353.1	n.379+8022C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31420 AN: 150806 Hom.: 5046 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00747

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.209 AC: 31481 AN: 150924 Hom.: 5068 Cov.: 31 AF XY: 0.204 AC XY: 15068 AN XY: 73702

African (AFR) AF: 0.458 AC: 18883 AN: 41190

American (AMR) AF: 0.134 AC: 2019 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 622 AN: 3454

East Asian (EAS) AF: 0.00748 AC: 38 AN: 5078

South Asian (SAS) AF: 0.125 AC: 599 AN: 4782

European-Finnish (FIN) AF: 0.0991 AC: 1036 AN: 10452

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7725 AN: 67586

Other (OTH) AF: 0.184 AC: 385 AN: 2094

Alfa AF: 0.143 Hom.: 6139

Bravo AF: 0.221

Asia WGS AF: 0.0860 AC: 299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.19
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1161397; hg19: chr6-50596453;