chr4-102080492-G-T

Position:

• chr4-102080492-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 0.0381 in 152,006 control chromosomes in the GnomAD database, including 164 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 0.038 (164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0575 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: 0.0381 AC: 5789 AN: 151886 Hom.: 164 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00729

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0381 AC: 5787 AN: 152006 Hom.: 164 Cov.: 32 AF XY: 0.0366 AC XY: 2719 AN XY: 74302

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0493

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00729

Gnomad4 NFE AF: 0.0590

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0468 Hom.: 32

Bravo AF: 0.0421

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1813006; hg19: chr4-103001649;