ENST00000641631.1:n.548+1424A>G

Variant names:

• chr6-58326972-A-G
• rs9377831
• ENST00000641631.1:n.548+1424A>G

Variant summary

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

The ENST00000641631.1(ENSG00000225096):​n.548+1424A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,078 control chromosomes in the GnomAD database, including 1,613 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 0.12 (1613 hom., cov: 32)
• Consequence: ENSG00000225096 ENST00000641631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 3 publications found

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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
ENSG00000225096	ENST00000641631.1	n.548+1424A>G		intron_variant	Intron 6 of 6
ENSG00000225096	ENST00000641775.1	n.457-109587A>G		intron_variant	Intron 4 of 5
ENSG00000225096	ENST00000661843.1	n.525+1424A>G		intron_variant	Intron 6 of 6
ENSG00000225096	ENST00000670654.1	n.449-28173A>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17934 AN: 151960 Hom.: 1612 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.118 AC: 17954 AN: 152078 Hom.: 1613 Cov.: 32 AF XY: 0.119 AC XY: 8878 AN XY: 74352

African (AFR) AF: 0.0748 AC: 3108 AN: 41534

American (AMR) AF: 0.286 AC: 4357 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1740 AN: 5150

South Asian (SAS) AF: 0.0441 AC: 213 AN: 4828

European-Finnish (FIN) AF: 0.0790 AC: 837 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7079 AN: 67956

Other (OTH) AF: 0.128 AC: 270 AN: 2104

Alfa AF: 0.129 Hom.: 340

Bravo AF: 0.135

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs9377831; hg19: chr6-58653250;