rs6928844

chr6-114748553-C-Gchr6-114748553-C-T

Variant summary

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

The variant allele was found at a frequency of 0.153 in 151,992 control chromosomes in the GnomAD database, including 2,034 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 0.15 (2034 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 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: 0.153 AC: 23247 AN: 151872 Hom.: 2034 Cov.: 32

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.153 AC: 23243 AN: 151992 Hom.: 2034 Cov.: 32 AF XY: 0.151 AC XY: 11242 AN XY: 74296

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.160

Alfa AF: 0.0611 Hom.: 75

Bravo AF: 0.144

Asia WGS AF: 0.106 AC: 370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.16
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6928844; hg19: chr6-115069717;