rs4604307

Variant names:

• chr6-33057894-C-G
• rs4604307

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 0.29 in 152,042 control chromosomes in the GnomAD database, including 8,457 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 0.29 (8457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.290 AC: 44033 AN: 151924 Hom.: 8438 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.290 AC: 44083 AN: 152042 Hom.: 8457 Cov.: 31 AF XY: 0.288 AC XY: 21371 AN XY: 74320

African (AFR) AF: 0.497 AC: 20605 AN: 41432

American (AMR) AF: 0.246 AC: 3759 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3569 AN: 5180

South Asian (SAS) AF: 0.342 AC: 1649 AN: 4820

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11994 AN: 67960

Other (OTH) AF: 0.309 AC: 652 AN: 2108

Alfa AF: 0.221 Hom.: 619

Bravo AF: 0.308

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.45
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4604307; hg19: chr6-33025671;