chr6-54400598-T-C

Variant names:

• chr6-54400598-T-C
• rs16885294

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 0.0797 in 152,090 control chromosomes in the GnomAD database, including 836 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 0.080 (836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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: 0.0796 AC: 12095 AN: 151972 Hom.: 831 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.0349

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0797 AC: 12119 AN: 152090 Hom.: 836 Cov.: 32 AF XY: 0.0780 AC XY: 5802 AN XY: 74342

African (AFR) AF: 0.186 AC: 7720 AN: 41476

American (AMR) AF: 0.0752 AC: 1147 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3468

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5170

South Asian (SAS) AF: 0.0347 AC: 167 AN: 4810

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0354 AC: 2405 AN: 67998

Other (OTH) AF: 0.0693 AC: 146 AN: 2108

Alfa AF: 0.0500 Hom.: 1019

Bravo AF: 0.0892

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs16885294; hg19: chr6-54265396;