chr2-75041353-A-G

Position:

• chr2-75041353-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.502

Alfa AF: 0.532 Hom.: 28669

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2422090; hg19: chr2-75268480;