rs4692845

Positions:

• chr4-170614130-G-A
• chr4-170614130-G-T

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 0.487 in 151,966 control chromosomes in the GnomAD database, including 22,213 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 0.49 (22213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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: 0.487 AC: 73903 AN: 151848 Hom.: 22161 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.487 AC: 74011 AN: 151966 Hom.: 22213 Cov.: 32 AF XY: 0.479 AC XY: 35569 AN XY: 74236

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.473

Alfa AF: 0.425 Hom.: 2475

Bravo AF: 0.526

Asia WGS AF: 0.262 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4692845; hg19: chr4-171535281;