Variant chr1-72285502-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000665984.1(ENSG00000286863):n.153+2097T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,064 control chromosomes in the GnomAD database, including 30,327 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 0.62 ( 30327 hom., cov: 33)

Consequence

ENST00000665984.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.699

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105378797	XR_001737670.2 linkuse as main transcript	n.472+2097T>C	intron_variant, non_coding_transcript_variant
LOC105378797	XR_001737671.3 linkuse as main transcript	n.472+2097T>C	intron_variant, non_coding_transcript_variant
LOC105378797	XR_947505.3 linkuse as main transcript	n.472+2097T>C	intron_variant, non_coding_transcript_variant
LOC105378797	XR_947506.3 linkuse as main transcript	n.472+2097T>C	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect
ENST00000665984.1 linkuse as main transcript	n.153+2097T>C	intron_variant, non_coding_transcript_variant
ENST00000653965.1 linkuse as main transcript	n.236+2097T>C	intron_variant, non_coding_transcript_variant
ENST00000667836.1 linkuse as main transcript	n.227+2097T>C	intron_variant, non_coding_transcript_variant
ENST00000688733.1 linkuse as main transcript	n.56+2097T>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.625

AC:

94968

AN:

151946

Hom.:

30313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.556

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.735

Gnomad EAS

AF:

0.924

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.649

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.639

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

GnomAD4 genome

AF:

0.625

AC:

95014

AN:

152064

Hom.:

30327

Cov.:

AF XY:

0.631

AC XY:

46931

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.540

Gnomad4 AMR

AF:

0.708

Gnomad4 ASJ

AF:

0.735

Gnomad4 EAS

AF:

0.923

Gnomad4 SAS

AF:

0.668

Gnomad4 FIN

AF:

0.649

Gnomad4 NFE

AF:

0.623

Gnomad4 OTH

AF:

0.643

Alfa

AF:

0.632

Hom.:

41071

Bravo

AF:

0.628

Asia WGS

AF:

0.752

AC:

2613

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.80

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