rs1455201

Variant names:

• chr6-104242516-T-C
• rs1455201

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 0.56 in 151,970 control chromosomes in the GnomAD database, including 25,871 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 0.56 (25871 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -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 = 0.786 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: 0.560 AC: 85072 AN: 151852 Hom.: 25828 Cov.: 31

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.560 AC: 85166 AN: 151970 Hom.: 25871 Cov.: 31 AF XY: 0.554 AC XY: 41126 AN XY: 74274

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.507

Alfa AF: 0.541 Hom.: 2887

Bravo AF: 0.571

Asia WGS AF: 0.300 AC: 1044 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	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455201; hg19: chr6-104690391; COSMIC: COSV69418512;