6-149420078-G-T

Variant names:

• chr6-149420078-G-T
• rs9485389

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 0.236 in 152,126 control chromosomes in the GnomAD database, including 4,427 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 0.24 (4427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35866 AN: 152008 Hom.: 4417 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.236 AC: 35904 AN: 152126 Hom.: 4427 Cov.: 32 AF XY: 0.233 AC XY: 17344 AN XY: 74372

African (AFR) AF: 0.221 AC: 9155 AN: 41494

American (AMR) AF: 0.215 AC: 3281 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3470

East Asian (EAS) AF: 0.0880 AC: 456 AN: 5180

South Asian (SAS) AF: 0.191 AC: 921 AN: 4818

European-Finnish (FIN) AF: 0.248 AC: 2623 AN: 10562

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17668 AN: 67988

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.248 Hom.: 654

Bravo AF: 0.235

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs9485389; hg19: chr6-149741214; COSMIC: COSV60291717;