rs4949168

Positions:

• chr1-5115776-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.44 (2371 hom., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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: 0.00 AC: 56386 AN: 129610 Hom.: 2376 Cov.: 22 FAILED QC

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.429

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.435 AC: 56423 AN: 129686 Hom.: 2371 Cov.: 22 AF XY: 0.433 AC XY: 27068 AN XY: 62464

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.429

Alfa AF: 0.409 Hom.: 124

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4949168; hg19: chr1-5175836;