chr4-110818136-A-G

Variant names:

• chr4-110818136-A-G
• rs10516564

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 0.251 in 151,864 control chromosomes in the GnomAD database, including 5,211 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 0.25 (5211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 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: 0.251 AC: 38050 AN: 151746 Hom.: 5209 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.251 AC: 38071 AN: 151864 Hom.: 5211 Cov.: 32 AF XY: 0.247 AC XY: 18316 AN XY: 74244

African (AFR) AF: 0.137 AC: 5685 AN: 41470

American (AMR) AF: 0.311 AC: 4725 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1230 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1176 AN: 5162

South Asian (SAS) AF: 0.191 AC: 920 AN: 4816

European-Finnish (FIN) AF: 0.261 AC: 2768 AN: 10592

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20611 AN: 67828

Other (OTH) AF: 0.270 AC: 569 AN: 2108

Alfa AF: 0.289 Hom.: 6705

Bravo AF: 0.251

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.75
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs10516564; hg19: chr4-111739292;