rs10003577

chr4-94398928-G-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 0.215 in 151,980 control chromosomes in the GnomAD database, including 9,004 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 0.21 (9004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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: 0.214 AC: 32507 AN: 151860 Hom.: 8964 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0624

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.215 AC: 32605 AN: 151980 Hom.: 9004 Cov.: 32 AF XY: 0.213 AC XY: 15833 AN XY: 74320

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0614

Gnomad4 FIN AF: 0.0346

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.170

Alfa AF: 0.128 Hom.: 665

Bravo AF: 0.251

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.11
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10003577; hg19: chr4-95320079;