rs826132

Variant names:

• chr2-183911997-G-A
• rs826132
• ENST00000441026.1:n.103+7366G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-183911997-G-A
• chr2-183911997-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441026.1(ENSG00000234172):​n.103+7366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,902 control chromosomes in the GnomAD database, including 9,829 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 0.35 (9829 hom., cov: 33)
• Consequence: ENSG00000234172 ENST00000441026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 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
ENSG00000234172	ENST00000441026.1	n.103+7366G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53680 AN: 151786 Hom.: 9817 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.354 AC: 53716 AN: 151902 Hom.: 9829 Cov.: 33 AF XY: 0.357 AC XY: 26490 AN XY: 74242

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.374

Alfa AF: 0.365 Hom.: 1284

Bravo AF: 0.355

Asia WGS AF: 0.377 AC: 1299 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.86
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826132; hg19: chr2-184776724;