4-40330821-T-A

Position:

• chr4-40330821-T-A

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 0.205 in 152,114 control chromosomes in the GnomAD database, including 3,642 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 0.20 (3642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31150 AN: 151996 Hom.: 3644 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.205 AC: 31149 AN: 152114 Hom.: 3642 Cov.: 32 AF XY: 0.208 AC XY: 15452 AN XY: 74340

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.209

Alfa AF: 0.220 Hom.: 528

Bravo AF: 0.202

Asia WGS AF: 0.164 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10805117; hg19: chr4-40332838;