4-60622768-T-C

Variant names:

• chr4-60622768-T-C
• rs1561478

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 0.837 in 152,086 control chromosomes in the GnomAD database, including 53,515 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 0.84 (53515 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127258 AN: 151968 Hom.: 53485 Cov.: 30

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.837 AC: 127335 AN: 152086 Hom.: 53515 Cov.: 30 AF XY: 0.841 AC XY: 62488 AN XY: 74324

African (AFR) AF: 0.770 AC: 31923 AN: 41462

American (AMR) AF: 0.869 AC: 13288 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2737 AN: 3470

East Asian (EAS) AF: 0.969 AC: 4988 AN: 5146

South Asian (SAS) AF: 0.848 AC: 4086 AN: 4816

European-Finnish (FIN) AF: 0.891 AC: 9429 AN: 10584

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58068 AN: 68000

Other (OTH) AF: 0.852 AC: 1800 AN: 2112

Alfa AF: 0.841 Hom.: 11629

Bravo AF: 0.832

Asia WGS AF: 0.904 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.49
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1561478; hg19: chr4-61488486;