rs4463232

Variant names:

• chr6-85448442-T-G
• rs4463232

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 0.169 in 152,100 control chromosomes in the GnomAD database, including 2,415 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 0.17 (2415 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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: 0.169 AC: 25673 AN: 151982 Hom.: 2418 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.169 AC: 25683 AN: 152100 Hom.: 2415 Cov.: 33 AF XY: 0.165 AC XY: 12237 AN XY: 74384

African (AFR) AF: 0.249 AC: 10321 AN: 41464

American (AMR) AF: 0.127 AC: 1942 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3468

East Asian (EAS) AF: 0.0617 AC: 319 AN: 5174

South Asian (SAS) AF: 0.168 AC: 810 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1115 AN: 10582

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10108 AN: 67992

Other (OTH) AF: 0.154 AC: 325 AN: 2106

Alfa AF: 0.160 Hom.: 283

Bravo AF: 0.172

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4463232; hg19: chr6-86158160;