chr2-225882961-G-C

Variant names:

• chr2-225882961-G-C
• rs13022222
• ENST00000762654.1:n.174+2696C>G

Variant summary

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

The ENST00000762654.1(ENSG00000299331):​n.174+2696C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,884 control chromosomes in the GnomAD database, including 4,935 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 0.23 (4935 hom., cov: 32)
• Consequence: ENSG00000299331 ENST00000762654.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 5 publications found

Genes affected

ENSG00000299331 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985992	XR_001739907.2	n.99-1323G>C		intron_variant	Intron 1 of 2
LOC105373914	XR_007088108.1	n.254+2696C>G		intron_variant	Intron 2 of 3
LOC105373914	XR_007088109.1	n.254+2696C>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299331	ENST00000762654.1	n.174+2696C>G		intron_variant	Intron 1 of 2
ENSG00000299331	ENST00000762655.1	n.175+2696C>G		intron_variant	Intron 1 of 2
ENSG00000299331	ENST00000762656.1	n.174+2696C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34246 AN: 151766 Hom.: 4905 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.226 AC: 34339 AN: 151884 Hom.: 4935 Cov.: 32 AF XY: 0.225 AC XY: 16737 AN XY: 74226

African (AFR) AF: 0.410 AC: 16972 AN: 41430

American (AMR) AF: 0.134 AC: 2050 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1077 AN: 5122

South Asian (SAS) AF: 0.276 AC: 1327 AN: 4814

European-Finnish (FIN) AF: 0.120 AC: 1275 AN: 10582

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10558 AN: 67912

Other (OTH) AF: 0.187 AC: 395 AN: 2110

Alfa AF: 0.0786 Hom.: 94

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.37
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs13022222; hg19: chr2-226747677;