chr4-110713670-C-T

Variant names:

• chr4-110713670-C-T
• rs10222783

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 0.161 in 151,722 control chromosomes in the GnomAD database, including 2,982 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 0.16 (2982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.161 AC: 24352 AN: 151604 Hom.: 2968 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.0650

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0311

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.161 AC: 24394 AN: 151722 Hom.: 2982 Cov.: 32 AF XY: 0.159 AC XY: 11765 AN XY: 74112

African (AFR) AF: 0.312 AC: 12906 AN: 41352

American (AMR) AF: 0.212 AC: 3221 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0650 AC: 225 AN: 3462

East Asian (EAS) AF: 0.327 AC: 1672 AN: 5118

South Asian (SAS) AF: 0.145 AC: 696 AN: 4812

European-Finnish (FIN) AF: 0.0311 AC: 328 AN: 10538

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0741 AC: 5034 AN: 67906

Other (OTH) AF: 0.139 AC: 292 AN: 2102

Alfa AF: 0.107 Hom.: 3833

Bravo AF: 0.184

Asia WGS AF: 0.205 AC: 712 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10222783; hg19: chr4-111634826;