6-23925552-T-C

Variant names:

• chr6-23925552-T-C
• rs482180

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 0.141 in 152,124 control chromosomes in the GnomAD database, including 2,029 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 (2029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 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: 0.141 AC: 21447 AN: 152006 Hom.: 2029 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00384

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.0909

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.141 AC: 21456 AN: 152124 Hom.: 2029 Cov.: 32 AF XY: 0.137 AC XY: 10219 AN XY: 74374

African (AFR) AF: 0.265 AC: 10963 AN: 41430

American (AMR) AF: 0.112 AC: 1712 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3464

East Asian (EAS) AF: 0.00385 AC: 20 AN: 5190

South Asian (SAS) AF: 0.0568 AC: 274 AN: 4828

European-Finnish (FIN) AF: 0.0909 AC: 964 AN: 10600

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0997 AC: 6782 AN: 68008

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.137 Hom.: 211

Bravo AF: 0.148

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.57
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs482180; hg19: chr6-23925780;