4-34893828-A-G

Variant names:

• chr4-34893828-A-G
• rs11722719

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 0.678 in 151,874 control chromosomes in the GnomAD database, including 35,184 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 0.68 (35184 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.678 AC: 102933 AN: 151756 Hom.: 35143 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.678 AC: 103033 AN: 151874 Hom.: 35184 Cov.: 31 AF XY: 0.683 AC XY: 50681 AN XY: 74230

African (AFR) AF: 0.662 AC: 27424 AN: 41412

American (AMR) AF: 0.721 AC: 11010 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2233 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4784 AN: 5162

South Asian (SAS) AF: 0.780 AC: 3762 AN: 4820

European-Finnish (FIN) AF: 0.651 AC: 6857 AN: 10530

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44772 AN: 67904

Other (OTH) AF: 0.662 AC: 1399 AN: 2112

Alfa AF: 0.670 Hom.: 13442

Bravo AF: 0.680

Asia WGS AF: 0.792 AC: 2755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11722719; hg19: chr4-34895450;