chr2-75041353-A-G

Variant names:

• chr2-75041353-A-G
• rs2422090

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 0.505 in 152,068 control chromosomes in the GnomAD database, including 19,691 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 0.51 (19691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 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: 0.505 AC: 76768 AN: 151950 Hom.: 19668 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.505 AC: 76835 AN: 152068 Hom.: 19691 Cov.: 32 AF XY: 0.500 AC XY: 37193 AN XY: 74326

African (AFR) AF: 0.481 AC: 19937 AN: 41462

American (AMR) AF: 0.482 AC: 7363 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2148 AN: 5172

South Asian (SAS) AF: 0.338 AC: 1627 AN: 4820

European-Finnish (FIN) AF: 0.473 AC: 5000 AN: 10576

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36785 AN: 67974

Other (OTH) AF: 0.502 AC: 1061 AN: 2112

Alfa AF: 0.530 Hom.: 36263

Bravo AF: 0.505

Asia WGS AF: 0.374 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2422090; hg19: chr2-75268480;