4-10277044-G-C

Variant names:

• chr4-10277044-G-C
• rs10489069

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 0.178 in 152,124 control chromosomes in the GnomAD database, including 3,080 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 (3080 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 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: 0.178 AC: 27043 AN: 152006 Hom.: 3077 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.178 AC: 27039 AN: 152124 Hom.: 3080 Cov.: 32 AF XY: 0.175 AC XY: 13006 AN XY: 74358

African (AFR) AF: 0.0459 AC: 1908 AN: 41526

American (AMR) AF: 0.175 AC: 2667 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3470

East Asian (EAS) AF: 0.125 AC: 647 AN: 5166

South Asian (SAS) AF: 0.166 AC: 799 AN: 4814

European-Finnish (FIN) AF: 0.204 AC: 2154 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16838 AN: 67966

Other (OTH) AF: 0.217 AC: 458 AN: 2112

Alfa AF: 0.0709 Hom.: 109

Bravo AF: 0.173

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.37
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs10489069; hg19: chr4-10278668; COSMIC: COSV50688584;