rs2092331

Variant names:

• chr22-35235551-C-T
• rs2092331
• ENST00000794420.1:n.201-2660G>A

Variant summary

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

The ENST00000794420.1(ENSG00000303430):​n.201-2660G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0744 in 152,140 control chromosomes in the GnomAD database, including 586 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 0.074 (586 hom., cov: 31)
• Consequence: ENSG00000303430 ENST00000794420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 5 publications found

Genes affected

ENSG00000303430 (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 (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794420.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303430	ENST00000794420.1		n.201-2660G>A		intron	N/A
	ENSG00000303430	ENST00000794421.1		n.212-2660G>A		intron	N/A
	ENSG00000303430	ENST00000794422.1		n.261-2660G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11315 AN: 152022 Hom.: 588 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0744 AC: 11323 AN: 152140 Hom.: 586 Cov.: 31 AF XY: 0.0734 AC XY: 5460 AN XY: 74388

African (AFR) AF: 0.145 AC: 6021 AN: 41482

American (AMR) AF: 0.0663 AC: 1013 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3472

East Asian (EAS) AF: 0.140 AC: 725 AN: 5182

South Asian (SAS) AF: 0.0486 AC: 234 AN: 4814

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0414 AC: 2816 AN: 67988

Other (OTH) AF: 0.0568 AC: 120 AN: 2112

Alfa AF: 0.0501 Hom.: 457

Bravo AF: 0.0789

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2092331;

hg19: chr22-35631544;