chr2-183911997-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441026.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234172	ENST00000441026.1	TSL:2	n.103+7366G>A		intron	N/A
	ENSG00000234172	ENST00000828168.1		n.139+7366G>A		intron	N/A

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

African (AFR) AF: 0.271 AC: 11222 AN: 41456

American (AMR) AF: 0.443 AC: 6745 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1506 AN: 5172

South Asian (SAS) AF: 0.453 AC: 2185 AN: 4826

European-Finnish (FIN) AF: 0.340 AC: 3585 AN: 10538

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25923 AN: 67890

Other (OTH) AF: 0.374 AC: 789 AN: 2110

Alfa AF: 0.361 Hom.: 1316

Bravo AF: 0.355

Asia WGS AF: 0.377 AC: 1299 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.86
DANN	Benign	0.14
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs826132; hg19: chr2-184776724;