4-60905713-A-G

Position:

• chr4-60905713-A-G

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 0.11 in 152,108 control chromosomes in the GnomAD database, including 1,046 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 0.11 (1046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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: 0.110 AC: 16777 AN: 151990 Hom.: 1043 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.110 AC: 16798 AN: 152108 Hom.: 1046 Cov.: 32 AF XY: 0.108 AC XY: 8028 AN XY: 74360

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0159

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.127

Alfa AF: 0.121 Hom.: 1633

Bravo AF: 0.112

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455280; hg19: chr4-61771431;