chr4-60096703-C-T

Position:

• chr4-60096703-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.92 in 152,234 control chromosomes in the GnomAD database, including 64,587 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 0.92 (64587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139963 AN: 152116 Hom.: 64546 Cov.: 33

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.920 AC: 140052 AN: 152234 Hom.: 64587 Cov.: 33 AF XY: 0.922 AC XY: 68612 AN XY: 74432

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.923

Alfa AF: 0.939 Hom.: 34230

Bravo AF: 0.916

Asia WGS AF: 0.902 AC: 3138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.059
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372206; hg19: chr4-60962421;