9-6213468-C-T

Variant names:

• chr9-6213468-C-T
• rs7848215

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 0.345 in 151,738 control chromosomes in the GnomAD database, including 11,007 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 0.34 (11007 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52255 AN: 151620 Hom.: 10983 Cov.: 29

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.345 AC: 52331 AN: 151738 Hom.: 11007 Cov.: 29 AF XY: 0.341 AC XY: 25318 AN XY: 74148

African (AFR) AF: 0.591 AC: 24447 AN: 41362

American (AMR) AF: 0.242 AC: 3697 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3466

East Asian (EAS) AF: 0.0741 AC: 381 AN: 5142

South Asian (SAS) AF: 0.274 AC: 1317 AN: 4806

European-Finnish (FIN) AF: 0.260 AC: 2725 AN: 10490

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17532 AN: 67918

Other (OTH) AF: 0.316 AC: 664 AN: 2098

Alfa AF: 0.273 Hom.: 5953

Bravo AF: 0.357

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.9
DANN	Benign	0.19
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs7848215; hg19: chr9-6213468;