chr2-54687322-C-T

Variant names:

• chr2-54687322-C-T
• rs2941577

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 0.0956 in 152,230 control chromosomes in the GnomAD database, including 745 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 0.096 (745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 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: 0.0957 AC: 14552 AN: 152112 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0938

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0956 AC: 14554 AN: 152230 Hom.: 745 Cov.: 32 AF XY: 0.0941 AC XY: 7001 AN XY: 74438

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0935

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.107

Alfa AF: 0.106 Hom.: 760

Bravo AF: 0.0966

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2941577; hg19: chr2-54914459;