chr4-35409009-T-C

Position:

• chr4-35409009-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.44 in 152,008 control chromosomes in the GnomAD database, including 17,108 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 0.44 (17108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66867 AN: 151890 Hom.: 17111 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.440 AC: 66871 AN: 152008 Hom.: 17108 Cov.: 32 AF XY: 0.443 AC XY: 32941 AN XY: 74286

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.476

Alfa AF: 0.536 Hom.: 34488

Bravo AF: 0.431

Asia WGS AF: 0.523 AC: 1817 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533317; hg19: chr4-35410631;