rs10003577

Variant names:

• chr4-94398928-G-C
• rs10003577

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.631 AC: 26148 AN: 41410

American (AMR) AF: 0.221 AC: 3365 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1010 AN: 5172

South Asian (SAS) AF: 0.0614 AC: 296 AN: 4822

European-Finnish (FIN) AF: 0.0346 AC: 366 AN: 10576

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0137 AC: 932 AN: 67954

Other (OTH) AF: 0.170 AC: 358 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10003577; hg19: chr4-95320079;