rs4420371

Variant names:

• chr13-30766496-G-C
• rs4420371

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 0.232 in 152,048 control chromosomes in the GnomAD database, including 4,517 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 0.23 (4517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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: 0.232 AC: 35242 AN: 151930 Hom.: 4514 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.232 AC: 35259 AN: 152048 Hom.: 4517 Cov.: 32 AF XY: 0.237 AC XY: 17580 AN XY: 74306

African (AFR) AF: 0.119 AC: 4944 AN: 41478

American (AMR) AF: 0.263 AC: 4026 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2160 AN: 5150

South Asian (SAS) AF: 0.296 AC: 1424 AN: 4810

European-Finnish (FIN) AF: 0.269 AC: 2846 AN: 10562

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.267 AC: 18127 AN: 67980

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.242 Hom.: 609

Bravo AF: 0.229

Asia WGS AF: 0.356 AC: 1238 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	0.82
DANN	Benign	0.48
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4420371; hg19: chr13-31340633;