rs1054998

Positions:

• chr5-170188494-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 0.351 in 152,046 control chromosomes in the GnomAD database, including 9,757 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 0.35 (9757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

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 (AMR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53260 AN: 151928 Hom.: 9736 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.351 AC: 53321 AN: 152046 Hom.: 9757 Cov.: 32 AF XY: 0.351 AC XY: 26078 AN XY: 74318

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.376

Alfa AF: 0.381 Hom.: 22601

Bravo AF: 0.349

Asia WGS AF: 0.310 AC: 1080 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	3.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1054998; hg19: chr5-169615498; COSMIC: COSV72584169;