6-55882170-C-T

Variant names:

• chr6-55882170-C-T
• rs1447132

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

The variant allele was found at a frequency of 0.503 in 151,622 control chromosomes in the GnomAD database, including 19,710 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 0.50 (19710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.552 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: 0.503 AC: 76211 AN: 151502 Hom.: 19698 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.503 AC: 76266 AN: 151622 Hom.: 19710 Cov.: 32 AF XY: 0.502 AC XY: 37210 AN XY: 74092

African (AFR) AF: 0.531 AC: 21977 AN: 41398

American (AMR) AF: 0.562 AC: 8520 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1846 AN: 3464

East Asian (EAS) AF: 0.159 AC: 819 AN: 5158

South Asian (SAS) AF: 0.373 AC: 1795 AN: 4816

European-Finnish (FIN) AF: 0.527 AC: 5556 AN: 10538

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33864 AN: 67798

Other (OTH) AF: 0.531 AC: 1115 AN: 2098

Alfa AF: 0.421 Hom.: 1819

Bravo AF: 0.506

Asia WGS AF: 0.307 AC: 1064 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.89
DANN	Benign	0.18
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs1447132; hg19: chr6-55746968;