chr6-30424471-T-C

Variant names:

• chr6-30424471-T-C
• rs9261925

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 0.163 in 152,040 control chromosomes in the GnomAD database, including 2,202 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 0.16 (2202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 13 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 = 0.234 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: 0.163 AC: 24730 AN: 151922 Hom.: 2202 Cov.: 31

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.163 AC: 24745 AN: 152040 Hom.: 2202 Cov.: 31 AF XY: 0.158 AC XY: 11741 AN XY: 74326

African (AFR) AF: 0.238 AC: 9860 AN: 41430

American (AMR) AF: 0.106 AC: 1622 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.0323 AC: 167 AN: 5178

South Asian (SAS) AF: 0.141 AC: 679 AN: 4820

European-Finnish (FIN) AF: 0.0888 AC: 939 AN: 10572

Middle Eastern (MID) AF: 0.0897 AC: 26 AN: 290

European-Non Finnish (NFE) AF: 0.155 AC: 10533 AN: 67976

Other (OTH) AF: 0.152 AC: 320 AN: 2108

Alfa AF: 0.154 Hom.: 3732

Bravo AF: 0.171

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs9261925; hg19: chr6-30392248;