chr5-171649223-G-A

Position:

• chr5-171649223-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.209 in 151,916 control chromosomes in the GnomAD database, including 3,682 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 0.21 (3682 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31726 AN: 151796 Hom.: 3681 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.209 AC: 31725 AN: 151916 Hom.: 3682 Cov.: 31 AF XY: 0.209 AC XY: 15494 AN XY: 74232

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.207

Alfa AF: 0.240 Hom.: 6131

Bravo AF: 0.203

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs254893; hg19: chr5-171076227; COSMIC: COSV60230939;