4-60296643-A-G

Variant names:

• chr4-60296643-A-G
• rs6816453

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 0.706 in 152,026 control chromosomes in the GnomAD database, including 39,701 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 0.71 (39701 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 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: 0.706 AC: 107276 AN: 151908 Hom.: 39702 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.706 AC: 107303 AN: 152026 Hom.: 39701 Cov.: 31 AF XY: 0.702 AC XY: 52206 AN XY: 74328

African (AFR) AF: 0.483 AC: 20001 AN: 41434

American (AMR) AF: 0.776 AC: 11849 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2804 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2565 AN: 5142

South Asian (SAS) AF: 0.608 AC: 2930 AN: 4818

European-Finnish (FIN) AF: 0.794 AC: 8403 AN: 10580

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56248 AN: 67992

Other (OTH) AF: 0.727 AC: 1536 AN: 2114

Alfa AF: 0.744 Hom.: 7525

Bravo AF: 0.698

Asia WGS AF: 0.522 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.81
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6816453; hg19: chr4-61162361;