8-30728221-G-T

Position:

• chr8-30728221-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.199 in 152,046 control chromosomes in the GnomAD database, including 3,195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.20 (3195 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 8-30728221-G-T is Benign according to our data. Variant chr8-30728221-G-T is described in ClinVar as [Benign]. Clinvar id is 1276408.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30728221G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30198 AN: 151928 Hom.: 3190 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.199 AC: 30236 AN: 152046 Hom.: 3195 Cov.: 32 AF XY: 0.201 AC XY: 14956 AN XY: 74326

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.169

Alfa AF: 0.173 Hom.: 3562

Bravo AF: 0.196

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.89
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: rs1002149; hg19: chr8-30585738;