4-10191803-C-G

Variant names:

• chr4-10191803-C-G
• rs10489080

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 0.182 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0521 AC: 2163 AN: 41540

American (AMR) AF: 0.179 AC: 2733 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.126 AC: 653 AN: 5166

South Asian (SAS) AF: 0.177 AC: 852 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2108 AN: 10506

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.251 AC: 17050 AN: 67944

Other (OTH) AF: 0.221 AC: 468 AN: 2114

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10489080; hg19: chr4-10193427;