rs3828610

chr5-150156062-A-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 0.487 in 150,962 control chromosomes in the GnomAD database, including 19,661 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 0.49 (19661 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 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: 0.487 AC: 73479 AN: 150848 Hom.: 19619 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.487 AC: 73587 AN: 150962 Hom.: 19661 Cov.: 31 AF XY: 0.484 AC XY: 35696 AN XY: 73684

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.495

Alfa AF: 0.453 Hom.: 1587

Bravo AF: 0.506

Asia WGS AF: 0.491 AC: 1707 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	19
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: rs3828610; hg19: chr5-149535625;