chr4-14905311-T-C

Variant names:

• chr4-14905311-T-C
• rs6815830

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 0.13 in 152,088 control chromosomes in the GnomAD database, including 1,533 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 0.13 (1533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 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: 0.130 AC: 19731 AN: 151970 Hom.: 1520 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.130 AC: 19781 AN: 152088 Hom.: 1533 Cov.: 32 AF XY: 0.128 AC XY: 9492 AN XY: 74358

African (AFR) AF: 0.215 AC: 8903 AN: 41496

American (AMR) AF: 0.101 AC: 1536 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3468

East Asian (EAS) AF: 0.0132 AC: 68 AN: 5152

South Asian (SAS) AF: 0.102 AC: 490 AN: 4820

European-Finnish (FIN) AF: 0.0793 AC: 841 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7037 AN: 67970

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.115 Hom.: 1469

Bravo AF: 0.134

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.60
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs6815830; hg19: chr4-14906935;