Variant rs6902485 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000403495.2(HMGB1P17):n.60T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.179 in 169,752 control chromosomes in the GnomAD database, including 6,497 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 0.19 ( 6323 hom., cov: 32)

Exomes 𝑓: 0.094 ( 174 hom. )

Consequence

HMGB1P17
ENST00000403495.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.25

Variant links:

Genes affected

HMGB1P17 (HGNC:39099): (high mobility group box 1 pseudogene 17)

HMGB1P17 links:

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

AHI1-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
AHI1-DT	NR_152842.1 linkuse as main transcript	n.315-5539A>G	intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1 linkuse as main transcript	n.201-5539A>G	intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1 linkuse as main transcript	n.315-5539A>G	intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1 linkuse as main transcript	n.439-5539A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HMGB1P17	ENST00000403495.2 linkuse as main transcript	n.60T>C		non_coding_transcript_exon_variant	1/1
AHI1-DT	ENST00000702072.1 linkuse as main transcript	n.148-5539A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28646

AN:

152000

Hom.:

6310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.0493

Gnomad SAS

AF:

0.0743

Gnomad FIN

AF:

0.00622

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.0435

Gnomad OTH

AF:

0.191

GnomAD4 exome

AF:

0.0942

AC:

1662

AN:

17634

Hom.:

174

Cov.:

AF XY:

0.0906

AC XY:

977

AN XY:

10780

show subpopulations

Gnomad4 AFR exome

AF:

0.636

Gnomad4 AMR exome

AF:

0.138

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.0643

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.0118

Gnomad4 NFE exome

AF:

0.0613

Gnomad4 OTH exome

AF:

0.0607

GnomAD4 genome

AF:

0.189

AC:

28713

AN:

152118

Hom.:

6323

Cov.:

AF XY:

0.182

AC XY:

13551

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.538

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.0492

Gnomad4 SAS

AF:

0.0745

Gnomad4 FIN

AF:

0.00622

Gnomad4 NFE

AF:

0.0434

Gnomad4 OTH

AF:

0.195

Alfa

AF:

0.0607

Hom.:

1005

Bravo

AF:

0.214

Asia WGS

AF:

0.122

AC:

422

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

2.2

DANN

Benign

0.36

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