Variant rs149970 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.243 in 488,550 control chromosomes in the GnomAD database, including 15,710 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 0.27 ( 6195 hom., cov: 32)

Exomes 𝑓: 0.23 ( 9515 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.849

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41227

AN:

151902

Hom.:

6172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.392

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.260

GnomAD4 exome

AF:

0.230

AC:

77368

AN:

336528

Hom.:

9515

AF XY:

0.229

AC XY:

41022

AN XY:

179218

show subpopulations

Gnomad4 AFR exome

AF:

0.397

Gnomad4 AMR exome

AF:

0.259

Gnomad4 ASJ exome

AF:

0.190

Gnomad4 EAS exome

AF:

0.245

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.225

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.272

AC:

41302

AN:

152022

Hom.:

6195

Cov.:

AF XY:

0.265

AC XY:

19724

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.393

Gnomad4 AMR

AF:

0.274

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.204

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.160

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.257

Alfa

AF:

0.243

Hom.:

603

Bravo

AF:

0.285

Asia WGS

AF:

0.229

AC:

799

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.70

DANN

Benign

0.68

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over