chr4-18033627-A-G

Variant names:

• chr4-18033627-A-G
• rs2061455

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 0.235 in 152,154 control chromosomes in the GnomAD database, including 5,269 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 (5269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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: 0.234 AC: 35607 AN: 152036 Hom.: 5242 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.235 AC: 35681 AN: 152154 Hom.: 5269 Cov.: 32 AF XY: 0.231 AC XY: 17163 AN XY: 74390

African (AFR) AF: 0.414 AC: 17188 AN: 41470

American (AMR) AF: 0.197 AC: 3014 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3472

East Asian (EAS) AF: 0.151 AC: 784 AN: 5188

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4822

European-Finnish (FIN) AF: 0.0959 AC: 1016 AN: 10596

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10744 AN: 68010

Other (OTH) AF: 0.227 AC: 479 AN: 2112

Alfa AF: 0.184 Hom.: 7209

Bravo AF: 0.249

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.72
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2061455; hg19: chr4-18035250;