chr6-23890463-G-A

Variant names:

• chr6-23890463-G-A
• rs953377

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 0.307 in 151,946 control chromosomes in the GnomAD database, including 7,417 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 (7417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46574 AN: 151828 Hom.: 7415 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.307 AC: 46606 AN: 151946 Hom.: 7417 Cov.: 32 AF XY: 0.305 AC XY: 22629 AN XY: 74266

African (AFR) AF: 0.342 AC: 14157 AN: 41436

American (AMR) AF: 0.228 AC: 3469 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1066 AN: 3466

East Asian (EAS) AF: 0.0604 AC: 312 AN: 5162

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4820

European-Finnish (FIN) AF: 0.333 AC: 3517 AN: 10570

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21821 AN: 67936

Other (OTH) AF: 0.309 AC: 653 AN: 2112

Alfa AF: 0.320 Hom.: 1039

Bravo AF: 0.298

Asia WGS AF: 0.185 AC: 643 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.37
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs953377; hg19: chr6-23890691;