rs4857008

chr3-67213420-C-T

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 0.549 in 152,022 control chromosomes in the GnomAD database, including 23,139 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 0.55 (23139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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: 0.549 AC: 83336 AN: 151902 Hom.: 23129 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.549 AC: 83395 AN: 152022 Hom.: 23139 Cov.: 32 AF XY: 0.544 AC XY: 40444 AN XY: 74300

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.554

Alfa AF: 0.543 Hom.: 10271

Bravo AF: 0.566

Asia WGS AF: 0.567 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.2
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4857008; hg19: chr3-67263844;