4-10181987-C-G

Variant names:

• chr4-10181987-C-G
• rs887729

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 0.266 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.345 AC: 14316 AN: 41466

American (AMR) AF: 0.211 AC: 3234 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3468

East Asian (EAS) AF: 0.128 AC: 661 AN: 5180

South Asian (SAS) AF: 0.179 AC: 862 AN: 4824

European-Finnish (FIN) AF: 0.199 AC: 2101 AN: 10582

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17114 AN: 68002

Other (OTH) AF: 0.280 AC: 592 AN: 2112

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs887729; hg19: chr4-10183611;