4-20115231-T-C

Variant names:

• chr4-20115231-T-C
• rs10516345

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 0.231 in 152,028 control chromosomes in the GnomAD database, including 4,606 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 0.23 (4606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.231 AC: 35097 AN: 151912 Hom.: 4588 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.231 AC: 35167 AN: 152028 Hom.: 4606 Cov.: 33 AF XY: 0.227 AC XY: 16892 AN XY: 74318

African (AFR) AF: 0.366 AC: 15174 AN: 41490

American (AMR) AF: 0.186 AC: 2837 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3472

East Asian (EAS) AF: 0.0945 AC: 488 AN: 5166

South Asian (SAS) AF: 0.176 AC: 847 AN: 4812

European-Finnish (FIN) AF: 0.157 AC: 1665 AN: 10590

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12679 AN: 67950

Other (OTH) AF: 0.211 AC: 445 AN: 2110

Alfa AF: 0.216 Hom.: 644

Bravo AF: 0.237

Asia WGS AF: 0.177 AC: 613 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.65
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs10516345; hg19: chr4-20116854;