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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373017	XR_007068085.1	n.471-2660G>A		intron_variant	Intron 3 of 3
LOC105373017	XR_007068086.1	n.3621-2660G>A		intron_variant	Intron 4 of 4
LOC105373017	XR_938209.3	n.322-2660G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303430	ENST00000794420.1	n.201-2660G>A		intron_variant	Intron 1 of 1
ENSG00000303430	ENST00000794421.1	n.212-2660G>A		intron_variant	Intron 2 of 2
ENSG00000303430	ENST00000794422.1	n.261-2660G>A		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2092331; hg19: chr22-35631544;