chr4-106513562-G-T

Variant names:

• chr4-106513562-G-T
• rs2903418

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 0.406 in 151,906 control chromosomes in the GnomAD database, including 12,645 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 0.41 (12645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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: 0.406 AC: 61607 AN: 151788 Hom.: 12628 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.406 AC: 61659 AN: 151906 Hom.: 12645 Cov.: 32 AF XY: 0.403 AC XY: 29920 AN XY: 74242

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.391

Alfa AF: 0.370 Hom.: 5600

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2903418; hg19: chr4-107434719;