6-23890649-T-C

Position:

• chr6-23890649-T-C

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 0.307 in 151,874 control chromosomes in the GnomAD database, including 7,412 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 0.31 (7412 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

ACMG classification

Verdict is Benign. Variant got -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 = 0.337 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: 0.307 AC: 46566 AN: 151756 Hom.: 7410 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.307 AC: 46598 AN: 151874 Hom.: 7412 Cov.: 31 AF XY: 0.305 AC XY: 22611 AN XY: 74178

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0584

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.309

Alfa AF: 0.305 Hom.: 14446

Bravo AF: 0.298

Asia WGS AF: 0.182 AC: 630 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	2.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4327688; hg19: chr6-23890877;