chr4-141488826-G-A

Position:

• chr4-141488826-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 0.221 in 152,112 control chromosomes in the GnomAD database, including 4,021 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 0.22 (4021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.221 AC: 33574 AN: 151994 Hom.: 4003 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.221 AC: 33644 AN: 152112 Hom.: 4021 Cov.: 32 AF XY: 0.220 AC XY: 16380 AN XY: 74358

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.210

Alfa AF: 0.204 Hom.: 705

Bravo AF: 0.234

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17007301; hg19: chr4-142409979;