4-60490835-T-C

Variant names:

• chr4-60490835-T-C
• rs9312054

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 0.0539 in 152,062 control chromosomes in the GnomAD database, including 378 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 0.054 (378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8185 AN: 151944 Hom.: 379 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0310

Gnomad FIN AF: 0.0243

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0539 AC: 8198 AN: 152062 Hom.: 378 Cov.: 32 AF XY: 0.0516 AC XY: 3837 AN XY: 74376

African (AFR) AF: 0.117 AC: 4855 AN: 41484

American (AMR) AF: 0.0251 AC: 384 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4828

European-Finnish (FIN) AF: 0.0243 AC: 258 AN: 10616

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2317 AN: 67892

Other (OTH) AF: 0.0460 AC: 97 AN: 2108

Alfa AF: 0.0607 Hom.: 229

Bravo AF: 0.0560

Asia WGS AF: 0.0170 AC: 57 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs9312054; hg19: chr4-61356553;