6-30098254-A-G

Variant names:

• chr6-30098254-A-G
• rs916570

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.519 AC: 21456 AN: 41378

American (AMR) AF: 0.292 AC: 4457 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1073 AN: 3466

East Asian (EAS) AF: 0.172 AC: 882 AN: 5130

South Asian (SAS) AF: 0.306 AC: 1474 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1151 AN: 10606

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 18020 AN: 67942

Other (OTH) AF: 0.345 AC: 724 AN: 2098

Alfa AF: 0.289 Hom.: 27535

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs916570; hg19: chr6-30066031;