6-23890537-G-A

Variant names:

• chr6-23890537-G-A
• rs953378

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 0.257 in 151,966 control chromosomes in the GnomAD database, including 5,490 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 0.26 (5490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39089 AN: 151848 Hom.: 5492 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.257 AC: 39095 AN: 151966 Hom.: 5490 Cov.: 32 AF XY: 0.257 AC XY: 19100 AN XY: 74246

African (AFR) AF: 0.176 AC: 7295 AN: 41484

American (AMR) AF: 0.204 AC: 3104 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1060 AN: 3466

East Asian (EAS) AF: 0.0580 AC: 299 AN: 5154

South Asian (SAS) AF: 0.262 AC: 1261 AN: 4820

European-Finnish (FIN) AF: 0.332 AC: 3508 AN: 10554

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21679 AN: 67926

Other (OTH) AF: 0.262 AC: 552 AN: 2108

Alfa AF: 0.279 Hom.: 835

Bravo AF: 0.242

Asia WGS AF: 0.170 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs953378; hg19: chr6-23890765;