chr4-10398532-G-A

Variant names:

• chr4-10398532-G-A
• rs4607209

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 0.868 in 140,928 control chromosomes in the GnomAD database, including 55,473 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 0.87 (55473 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973
• Publications: 8 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 (NFE) allele frequency at 95% confidence interval = 0.896 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: 0.868 AC: 122235 AN: 140814 Hom.: 55426 Cov.: 25

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.868 AC: 122342 AN: 140928 Hom.: 55473 Cov.: 25 AF XY: 0.864 AC XY: 59236 AN XY: 68550

African (AFR) AF: 0.876 AC: 35255 AN: 40244

American (AMR) AF: 0.779 AC: 10861 AN: 13946

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2582 AN: 3082

East Asian (EAS) AF: 0.628 AC: 3066 AN: 4880

South Asian (SAS) AF: 0.840 AC: 3683 AN: 4386

European-Finnish (FIN) AF: 0.885 AC: 8275 AN: 9348

Middle Eastern (MID) AF: 0.812 AC: 211 AN: 260

European-Non Finnish (NFE) AF: 0.902 AC: 56082 AN: 62172

Other (OTH) AF: 0.867 AC: 1621 AN: 1870

Alfa AF: 0.870 Hom.: 14291

Asia WGS AF: 0.779 AC: 2646 AN: 3394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.57
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs4607209; hg19: chr4-10400156;