1-5115776-A-G

Variant names:

• chr1-5115776-A-G
• rs4949168

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.435 AC: 56386 AN: 129610 Hom.: 2376 Cov.: 22

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

African (AFR) AF: 0.480 AC: 16467 AN: 34330

American (AMR) AF: 0.453 AC: 5775 AN: 12756

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1295 AN: 3028

East Asian (EAS) AF: 0.520 AC: 2323 AN: 4468

South Asian (SAS) AF: 0.449 AC: 1676 AN: 3734

European-Finnish (FIN) AF: 0.364 AC: 3192 AN: 8768

Middle Eastern (MID) AF: 0.368 AC: 89 AN: 242

European-Non Finnish (NFE) AF: 0.410 AC: 24515 AN: 59766

Other (OTH) AF: 0.429 AC: 742 AN: 1730

Alfa AF: 0.409 Hom.: 124

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

Other links and lift over

dbSNP: rs4949168; hg19: chr1-5175836;