chr6-23895602-C-T

Position:

• chr6-23895602-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;