chr5-155634515-A-G

Variant names:

• chr5-155634515-A-G
• rs2194711

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 0.185 in 152,018 control chromosomes in the GnomAD database, including 3,617 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 0.19 (3617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 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: 0.185 AC: 28094 AN: 151900 Hom.: 3608 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.185 AC: 28151 AN: 152018 Hom.: 3617 Cov.: 32 AF XY: 0.184 AC XY: 13705 AN XY: 74310

African (AFR) AF: 0.357 AC: 14778 AN: 41444

American (AMR) AF: 0.162 AC: 2471 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1070 AN: 5156

South Asian (SAS) AF: 0.205 AC: 986 AN: 4814

European-Finnish (FIN) AF: 0.0845 AC: 894 AN: 10574

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6820 AN: 67976

Other (OTH) AF: 0.184 AC: 388 AN: 2108

Alfa AF: 0.140 Hom.: 375

Bravo AF: 0.197

Asia WGS AF: 0.255 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2194711; hg19: chr5-155014075;