Genetic Variant ENSG00000223716:n.155-111T>C (chr9-38375218-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000422554.2(ENSG00000223716):n.155-111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,188 control chromosomes in the GnomAD database, including 40,182 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 0.71 ( 40176 hom., cov: 32)

Exomes 𝑓: 1.0 ( 6 hom. )

Consequence

ENSG00000223716
ENST00000422554.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.472

Variant links:

Genes affected

ENSG00000223716 (HGNC:):

ENSG00000223716 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=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107987065	XR_001746668.2 link	n.369-76T>C	intron_variant	Intron 2 of 3
LOC107987065	XR_001746669.2 link	n.269-76T>C	intron_variant	Intron 3 of 4
LOC107987065	XR_001746670.2 link	n.368+2241T>C	intron_variant	Intron 2 of 2
LOC105376040	XR_929605.1 link	n.321+55A>G	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223716	ENST00000422554.2 link	n.155-111T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108716

AN:

152056

Hom.:

40145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.929

Gnomad AMR

AF:

0.807

Gnomad ASJ

AF:

0.814

Gnomad EAS

AF:

0.790

Gnomad SAS

AF:

0.785

Gnomad FIN

AF:

0.841

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.746

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.715

AC:

108799

AN:

152176

Hom.:

40176

Cov.:

AF XY:

0.719

AC XY:

53527

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.508

Gnomad4 AMR

AF:

0.807

Gnomad4 ASJ

AF:

0.814

Gnomad4 EAS

AF:

0.789

Gnomad4 SAS

AF:

0.787

Gnomad4 FIN

AF:

0.841

Gnomad4 NFE

AF:

0.781

Gnomad4 OTH

AF:

0.747

Alfa

AF:

0.764

Hom.:

14054

Bravo

AF:

0.704

Asia WGS

AF:

0.780

AC:

2712

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.4

DANN

Benign

0.56

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