rs1455085

Variant names:

• chr6-66673715-A-G
• rs1455085

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 0.302 in 151,988 control chromosomes in the GnomAD database, including 7,197 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 0.30 (7197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 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: 0.302 AC: 45845 AN: 151870 Hom.: 7184 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.302 AC: 45891 AN: 151988 Hom.: 7197 Cov.: 32 AF XY: 0.306 AC XY: 22765 AN XY: 74304

African (AFR) AF: 0.252 AC: 10430 AN: 41456

American (AMR) AF: 0.402 AC: 6126 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3472

East Asian (EAS) AF: 0.157 AC: 807 AN: 5150

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4820

European-Finnish (FIN) AF: 0.364 AC: 3846 AN: 10578

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21452 AN: 67956

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.308 Hom.: 955

Bravo AF: 0.302

Asia WGS AF: 0.232 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1455085; hg19: chr6-67383608;