rs4694637

Positions:

• chr4-73747117-G-A

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 0.483 in 151,716 control chromosomes in the GnomAD database, including 19,108 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 0.48 (19108 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73747117G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73223 AN: 151598 Hom.: 19102 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.483 AC: 73258 AN: 151716 Hom.: 19108 Cov.: 32 AF XY: 0.490 AC XY: 36341 AN XY: 74122

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.500

Alfa AF: 0.473 Hom.: 2611

Bravo AF: 0.471

Asia WGS AF: 0.599 AC: 2082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4694637; hg19: chr4-74612834;