rs4473885

Variant names:

• chr6-132565393-C-T
• rs4473885

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 0.453 in 152,004 control chromosomes in the GnomAD database, including 16,232 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 0.45 (16232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.453 AC: 68769 AN: 151886 Hom.: 16223 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.453 AC: 68806 AN: 152004 Hom.: 16232 Cov.: 32 AF XY: 0.456 AC XY: 33850 AN XY: 74302

African (AFR) AF: 0.428 AC: 17727 AN: 41434

American (AMR) AF: 0.408 AC: 6223 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1624 AN: 3464

East Asian (EAS) AF: 0.852 AC: 4416 AN: 5186

South Asian (SAS) AF: 0.551 AC: 2653 AN: 4812

European-Finnish (FIN) AF: 0.393 AC: 4144 AN: 10552

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30536 AN: 67982

Other (OTH) AF: 0.471 AC: 993 AN: 2110

Alfa AF: 0.451 Hom.: 2231

Bravo AF: 0.454

Asia WGS AF: 0.699 AC: 2429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.23
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4473885; hg19: chr6-132886532;