4-10191803-C-G

Variant names:

• chr4-10191803-C-G
• rs10489080

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 0.182 in 152,046 control chromosomes in the GnomAD database, including 3,204 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 0.18 (3204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27613 AN: 151928 Hom.: 3201 Cov.: 32

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.182 AC: 27607 AN: 152046 Hom.: 3204 Cov.: 32 AF XY: 0.178 AC XY: 13252 AN XY: 74284

Gnomad4 AFR AF: 0.0521

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.221

Alfa AF: 0.0719 Hom.: 107

Bravo AF: 0.177

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489080; hg19: chr4-10193427;