rs1264314

chr6-30904120-T-Achr6-30904120-T-G

Variant summary

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

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 0.21 (103 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.207 AC: 3130 AN: 15122 Hom.: 101 Cov.: 0

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.0385

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.207 AC: 3143 AN: 15158 Hom.: 103 Cov.: 0 AF XY: 0.213 AC XY: 1539 AN XY: 7216

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0958

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.180

Alfa AF: 0.147 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.2
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1264314; hg19: chr6-30871897;