chr4-170614130-G-A

Variant names:

• chr4-170614130-G-A
• rs4692845

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.838 AC: 34743 AN: 41482

American (AMR) AF: 0.554 AC: 8456 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3466

East Asian (EAS) AF: 0.156 AC: 807 AN: 5162

South Asian (SAS) AF: 0.325 AC: 1560 AN: 4806

European-Finnish (FIN) AF: 0.221 AC: 2328 AN: 10524

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23223 AN: 67960

Other (OTH) AF: 0.473 AC: 1000 AN: 2112

Alfa AF: 0.438 Hom.: 2750

Bravo AF: 0.526

Asia WGS AF: 0.262 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.18
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs4692845; hg19: chr4-171535281;