6-23895602-C-T

Variant names:

• chr6-23895602-C-T
• rs1588549

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 0.281 in 151,910 control chromosomes in the GnomAD database, including 6,263 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 0.28 (6263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 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: 0.281 AC: 42601 AN: 151792 Hom.: 6260 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.281 AC: 42634 AN: 151910 Hom.: 6263 Cov.: 32 AF XY: 0.280 AC XY: 20783 AN XY: 74234

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.289

Alfa AF: 0.299 Hom.: 14890

Bravo AF: 0.268

Asia WGS AF: 0.178 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1588549; hg19: chr6-23895830;