4-108801970-G-A

Position:

• chr4-108801970-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 0.37 in 151,786 control chromosomes in the GnomAD database, including 10,463 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 0.37 (10463 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

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 (SAS) allele frequency at 95% confidence interval = 0.441 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: 0.370 AC: 56169 AN: 151668 Hom.: 10459 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.370 AC: 56197 AN: 151786 Hom.: 10463 Cov.: 31 AF XY: 0.376 AC XY: 27907 AN XY: 74172

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.378

Alfa AF: 0.361 Hom.: 15030

Bravo AF: 0.362

Asia WGS AF: 0.383 AC: 1330 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	2.1
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: rs4956211; hg19: chr4-109723126;