rs721412

Variant names:

• chr4-110026322-A-G
• rs721412

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 0.379 in 151,958 control chromosomes in the GnomAD database, including 11,498 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 0.38 (11498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 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: 0.379 AC: 57559 AN: 151838 Hom.: 11477 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.379 AC: 57637 AN: 151958 Hom.: 11498 Cov.: 32 AF XY: 0.380 AC XY: 28227 AN XY: 74274

African (AFR) AF: 0.485 AC: 20113 AN: 41434

American (AMR) AF: 0.405 AC: 6185 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3464

East Asian (EAS) AF: 0.508 AC: 2624 AN: 5164

South Asian (SAS) AF: 0.438 AC: 2109 AN: 4820

European-Finnish (FIN) AF: 0.302 AC: 3189 AN: 10562

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21135 AN: 67934

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.337 Hom.: 6572

Bravo AF: 0.396

Asia WGS AF: 0.482 AC: 1672 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.50
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs721412; hg19: chr4-110947478;