rs4505549

chr2-195423412-T-C

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 0.466 in 151,914 control chromosomes in the GnomAD database, including 19,861 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 0.47 (19861 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351

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 (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70844 AN: 151796 Hom.: 19866 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.466 AC: 70830 AN: 151914 Hom.: 19861 Cov.: 31 AF XY: 0.470 AC XY: 34856 AN XY: 74218

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.487

Alfa AF: 0.583 Hom.: 35155

Bravo AF: 0.435

Asia WGS AF: 0.426 AC: 1482 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	4.1
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4505549; hg19: chr2-196288136;