chr4-180070291-A-G

Position:

• chr4-180070291-A-G

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 0.0936 in 152,076 control chromosomes in the GnomAD database, including 912 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 0.094 (912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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: 0.0936 AC: 14230 AN: 151958 Hom.: 911 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0185

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0936 AC: 14230 AN: 152076 Hom.: 912 Cov.: 32 AF XY: 0.0895 AC XY: 6653 AN XY: 74334

Gnomad4 AFR AF: 0.0247

Gnomad4 AMR AF: 0.0750

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.000582

Gnomad4 SAS AF: 0.0185

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.100

Alfa AF: 0.130 Hom.: 1806

Bravo AF: 0.0873

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.054
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7680285; hg19: chr4-180991444;