4-60312113-C-T

Variant names:

• chr4-60312113-C-T
• rs6827408

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 0.697 in 151,914 control chromosomes in the GnomAD database, including 38,938 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 0.70 (38938 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.82 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: 0.697 AC: 105806 AN: 151794 Hom.: 38941 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.697 AC: 105824 AN: 151914 Hom.: 38938 Cov.: 31 AF XY: 0.693 AC XY: 51500 AN XY: 74264

African (AFR) AF: 0.455 AC: 18843 AN: 41408

American (AMR) AF: 0.766 AC: 11681 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2728 AN: 3468

East Asian (EAS) AF: 0.525 AC: 2696 AN: 5132

South Asian (SAS) AF: 0.600 AC: 2888 AN: 4814

European-Finnish (FIN) AF: 0.795 AC: 8408 AN: 10576

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56105 AN: 67954

Other (OTH) AF: 0.716 AC: 1509 AN: 2108

Alfa AF: 0.800 Hom.: 51092

Bravo AF: 0.687

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.087
DANN	Benign	0.66
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs6827408; hg19: chr4-61177831;