rs1078602

chr6-88118800-G-A

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 0.456 in 152,010 control chromosomes in the GnomAD database, including 16,534 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 0.46 (16534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 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: 0.456 AC: 69297 AN: 151890 Hom.: 16535 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.456 AC: 69326 AN: 152010 Hom.: 16534 Cov.: 32 AF XY: 0.453 AC XY: 33678 AN XY: 74288

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.414

Alfa AF: 0.453 Hom.: 3999

Bravo AF: 0.441

Asia WGS AF: 0.276 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.66
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: rs1078602; hg19: chr6-88828518;