5-110818610-T-C

Variant names:

• chr5-110818610-T-C
• rs3853750

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 0.296 in 151,984 control chromosomes in the GnomAD database, including 9,017 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 0.30 (9017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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: 0.296 AC: 44930 AN: 151866 Hom.: 8978 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.296 AC: 45028 AN: 151984 Hom.: 9017 Cov.: 32 AF XY: 0.297 AC XY: 22067 AN XY: 74282

African (AFR) AF: 0.575 AC: 23819 AN: 41448

American (AMR) AF: 0.229 AC: 3496 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3466

East Asian (EAS) AF: 0.219 AC: 1129 AN: 5166

South Asian (SAS) AF: 0.258 AC: 1246 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2142 AN: 10564

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11523 AN: 67952

Other (OTH) AF: 0.278 AC: 586 AN: 2108

Alfa AF: 0.223 Hom.: 1860

Bravo AF: 0.305

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.94
DANN	Benign	0.60
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3853750; hg19: chr5-110154309;