rs10016578

Variant names:

• chr4-18064723-C-T
• rs10016578

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 0.378 in 152,062 control chromosomes in the GnomAD database, including 17,107 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 0.38 (17107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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: 0.378 AC: 57368 AN: 151944 Hom.: 17041 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.378 AC: 57491 AN: 152062 Hom.: 17107 Cov.: 32 AF XY: 0.376 AC XY: 27925 AN XY: 74330

African (AFR) AF: 0.815 AC: 33798 AN: 41490

American (AMR) AF: 0.360 AC: 5496 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3466

East Asian (EAS) AF: 0.546 AC: 2825 AN: 5170

South Asian (SAS) AF: 0.165 AC: 794 AN: 4822

European-Finnish (FIN) AF: 0.158 AC: 1671 AN: 10552

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11180 AN: 67972

Other (OTH) AF: 0.367 AC: 776 AN: 2112

Alfa AF: 0.252 Hom.: 2019

Bravo AF: 0.415

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10016578; hg19: chr4-18066346;