chr4-10181987-C-G

Position:

• chr4-10181987-C-G

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 0.266 in 152,124 control chromosomes in the GnomAD database, including 5,657 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 0.27 (5657 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40429 AN: 152004 Hom.: 5645 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.266 AC: 40454 AN: 152124 Hom.: 5657 Cov.: 33 AF XY: 0.260 AC XY: 19331 AN XY: 74356

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.280

Alfa AF: 0.255 Hom.: 621

Bravo AF: 0.274

Asia WGS AF: 0.159 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.69
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs887729; hg19: chr4-10183611;