ENST00000846922.1:n.280+3118A>G

Variant names:

• chr10-4007811-A-G
• rs2031577
• ENST00000846922.1:n.280+3118A>G

Variant summary

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

The ENST00000846922.1(ENSG00000227101):​n.280+3118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,148 control chromosomes in the GnomAD database, including 24,320 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 0.54 (24320 hom., cov: 32)
• Consequence: ENSG00000227101 ENST00000846922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 11 publications found

Genes affected

ENSG00000227101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.67 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
ENSG00000227101	ENST00000846922.1	n.280+3118A>G		intron_variant	Intron 1 of 2
ENSG00000227101	ENST00000846923.1	n.249+3118A>G		intron_variant	Intron 1 of 1
ENSG00000227101	ENST00000846927.1	n.229+3118A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82272 AN: 152030 Hom.: 24302 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.541 AC: 82322 AN: 152148 Hom.: 24320 Cov.: 32 AF XY: 0.550 AC XY: 40914 AN XY: 74394

African (AFR) AF: 0.286 AC: 11868 AN: 41512

American (AMR) AF: 0.681 AC: 10421 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2121 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3375 AN: 5162

South Asian (SAS) AF: 0.651 AC: 3137 AN: 4820

European-Finnish (FIN) AF: 0.648 AC: 6861 AN: 10586

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.628 AC: 42674 AN: 67992

Other (OTH) AF: 0.578 AC: 1219 AN: 2110

Alfa AF: 0.599 Hom.: 121278

Bravo AF: 0.531

Asia WGS AF: 0.654 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.26
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2031577; hg19: chr10-4050003;