rs4702718

Positions:

• chr5-10670928-A-G

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 0.337 in 152,026 control chromosomes in the GnomAD database, including 9,124 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 0.34 (9124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.337 AC: 51222 AN: 151908 Hom.: 9111 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.337 AC: 51265 AN: 152026 Hom.: 9124 Cov.: 32 AF XY: 0.338 AC XY: 25129 AN XY: 74322

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.344

Alfa AF: 0.299 Hom.: 9370

Bravo AF: 0.345

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4702718; hg19: chr5-10671040;