rs6454676

Variant names:

• chr6-88167736-G-A
• rs6454676

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 0.144 in 152,224 control chromosomes in the GnomAD database, including 2,127 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 0.14 (2127 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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: 0.144 AC: 21978 AN: 152106 Hom.: 2125 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.144 AC: 21996 AN: 152224 Hom.: 2127 Cov.: 33 AF XY: 0.141 AC XY: 10522 AN XY: 74426

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.00560

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.123

Alfa AF: 0.108 Hom.: 475

Bravo AF: 0.150

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6454676; hg19: chr6-88877455;