rs4420962

Variant names:

• chr4-119099316-A-G
• rs4420962

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.263 AC: 10912 AN: 41510

American (AMR) AF: 0.230 AC: 3513 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3468

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5186

South Asian (SAS) AF: 0.240 AC: 1158 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2794 AN: 10552

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.301 AC: 20451 AN: 67958

Other (OTH) AF: 0.301 AC: 635 AN: 2112

Alfa AF: 0.281 Hom.: 2683

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
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4420962; hg19: chr4-120020471;