5-171701460-T-C

Variant names:

• chr5-171701460-T-C
• rs6555969

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.729 in 152,052 control chromosomes in the GnomAD database, including 41,203 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 0.73 (41203 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 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: 0.728 AC: 110668 AN: 151936 Hom.: 41150 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.729 AC: 110776 AN: 152052 Hom.: 41203 Cov.: 31 AF XY: 0.727 AC XY: 54042 AN XY: 74308

African (AFR) AF: 0.884 AC: 36692 AN: 41502

American (AMR) AF: 0.652 AC: 9951 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3468

East Asian (EAS) AF: 0.638 AC: 3285 AN: 5148

South Asian (SAS) AF: 0.642 AC: 3081 AN: 4800

European-Finnish (FIN) AF: 0.717 AC: 7595 AN: 10586

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45935 AN: 67966

Other (OTH) AF: 0.692 AC: 1457 AN: 2104

Alfa AF: 0.712 Hom.: 7313

Bravo AF: 0.732

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	16
DANN	Benign	0.61
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs6555969; hg19: chr5-171128464;