chr5-171588619-T-C

Variant names:

• chr5-171588619-T-C
• rs6892884

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 0.68 in 152,008 control chromosomes in the GnomAD database, including 35,640 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 0.68 (35640 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.751 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: 0.680 AC: 103356 AN: 151892 Hom.: 35626 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.680 AC: 103412 AN: 152008 Hom.: 35640 Cov.: 31 AF XY: 0.684 AC XY: 50861 AN XY: 74322

African (AFR) AF: 0.577 AC: 23894 AN: 41400

American (AMR) AF: 0.763 AC: 11661 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2952 AN: 3468

East Asian (EAS) AF: 0.771 AC: 3985 AN: 5170

South Asian (SAS) AF: 0.674 AC: 3244 AN: 4812

European-Finnish (FIN) AF: 0.732 AC: 7757 AN: 10590

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47569 AN: 67972

Other (OTH) AF: 0.695 AC: 1464 AN: 2106

Alfa AF: 0.685 Hom.: 49669

Bravo AF: 0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.7
DANN	Benign	0.84
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6892884; hg19: chr5-171015623;