rs826132

Positions:

• 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, non coding transcript 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: ENST00000441026.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000441026.1	n.103+7366G>A		intron_variant, non_coding_transcript_variant		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;