rs9468841

Variant names:

• chr6-30857510-T-C
• rs9468841

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 0.0992 in 152,224 control chromosomes in the GnomAD database, including 1,224 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 0.099 (1224 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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: 0.0991 AC: 15077 AN: 152104 Hom.: 1212 Cov.: 31

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0992 AC: 15097 AN: 152224 Hom.: 1224 Cov.: 31 AF XY: 0.106 AC XY: 7895 AN XY: 74412

African (AFR) AF: 0.0423 AC: 1758 AN: 41552

American (AMR) AF: 0.254 AC: 3876 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5170

South Asian (SAS) AF: 0.195 AC: 939 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1316 AN: 10586

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5202 AN: 68026

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.0935 Hom.: 1389

Bravo AF: 0.106

Asia WGS AF: 0.254 AC: 880 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	0.71
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9468841; hg19: chr6-30825287;