rs2413030

Variant names:

• chr22-31150965-G-A
• rs2413030

Your query was ambiguous. Multiple possible variants found:

• chr22-31150965-G-A
• chr22-31150965-G-C
• chr22-31150965-G-T

Variant summary

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

The variant allele was found at a frequency of 0.352 in 151,974 control chromosomes in the GnomAD database, including 10,646 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 (10646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53494 AN: 151856 Hom.: 10618 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.352 AC: 53562 AN: 151974 Hom.: 10646 Cov.: 32 AF XY: 0.363 AC XY: 26944 AN XY: 74286

African (AFR) AF: 0.436 AC: 18071 AN: 41428

American (AMR) AF: 0.454 AC: 6932 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3462

East Asian (EAS) AF: 0.776 AC: 4017 AN: 5176

South Asian (SAS) AF: 0.457 AC: 2199 AN: 4816

European-Finnish (FIN) AF: 0.336 AC: 3545 AN: 10544

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17070 AN: 67958

Other (OTH) AF: 0.353 AC: 744 AN: 2110

Alfa AF: 0.297 Hom.: 11436

Bravo AF: 0.363

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.79
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs2413030; hg19: chr22-31546951;