4-102630446-A-G

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 0.55 in 152,024 control chromosomes in the GnomAD database, including 23,399 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 (23399 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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: 83457 AN: 151906 Hom.: 23362 Cov.: 33

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.550 AC: 83541 AN: 152024 Hom.: 23399 Cov.: 33 AF XY: 0.548 AC XY: 40724 AN XY: 74290

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.548

Alfa AF: 0.513 Hom.: 30838

Bravo AF: 0.567

Asia WGS AF: 0.506 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7665090; hg19: chr4-103551603;