rs871153

chr4-102095721-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 0.288 in 152,110 control chromosomes in the GnomAD database, including 7,766 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 0.29 (7766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43842 AN: 151992 Hom.: 7769 Cov.: 32

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.288 AC: 43835 AN: 152110 Hom.: 7766 Cov.: 32 AF XY: 0.284 AC XY: 21080 AN XY: 74350

Gnomad4 AFR AF: 0.0818

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.327

Alfa AF: 0.372 Hom.: 5243

Bravo AF: 0.277

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	0.62
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs871153; hg19: chr4-103016878;