rs4420962

Positions:

• chr4-119099316-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 0.269 in 152,090 control chromosomes in the GnomAD database, including 5,811 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 0.27 (5811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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: 0.269 AC: 40953 AN: 151972 Hom.: 5813 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.269 AC: 40961 AN: 152090 Hom.: 5811 Cov.: 32 AF XY: 0.264 AC XY: 19615 AN XY: 74348

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.301

Alfa AF: 0.276 Hom.: 2128

Bravo AF: 0.267

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4420962; hg19: chr4-120020471;