rs714389

Positions:

• chr6-82871628-A-G

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 0.185 in 151,972 control chromosomes in the GnomAD database, including 3,260 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 0.19 (3260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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 (AMR) allele frequency at 95% confidence interval = 0.361 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: 0.185 AC: 28107 AN: 151854 Hom.: 3240 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.185 AC: 28167 AN: 151972 Hom.: 3260 Cov.: 31 AF XY: 0.187 AC XY: 13861 AN XY: 74280

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.193

Alfa AF: 0.144 Hom.: 393

Bravo AF: 0.213

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714389; hg19: chr6-83581347;