rs916570

Positions:

• chr6-30098254-A-G
• chr6-30098254-A-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 0.326 in 151,904 control chromosomes in the GnomAD database, including 9,364 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 0.33 (9364 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49535 AN: 151796 Hom.: 9355 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.326 AC: 49572 AN: 151904 Hom.: 9364 Cov.: 31 AF XY: 0.315 AC XY: 23399 AN XY: 74294

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.345

Alfa AF: 0.277 Hom.: 9306

Bravo AF: 0.354

Asia WGS AF: 0.241 AC: 824 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916570; hg19: chr6-30066031;