2-4675608-T-C

Position:

• chr2-4675608-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 0.85 in 152,252 control chromosomes in the GnomAD database, including 55,320 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 0.85 (55320 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 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: 0.850 AC: 129255 AN: 152136 Hom.: 55271 Cov.: 34

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.850 AC: 129362 AN: 152252 Hom.: 55320 Cov.: 34 AF XY: 0.847 AC XY: 63053 AN XY: 74418

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.839

Alfa AF: 0.766 Hom.: 2242

Bravo AF: 0.861

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285540; hg19: chr2-4723198;