Variant 5-80498283-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_205548.3(FAM151B):c.26-3509A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,146 control chromosomes in the GnomAD database, including 59,246 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 0.88 ( 59246 hom., cov: 30)

Consequence

FAM151B
NM_205548.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Variant links:

Genes affected

FAM151B (HGNC:33716): (family with sequence similarity 151 member B) Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

FAM151B 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
FAM151B	NM_205548.3 linkuse as main transcript	c.26-3509A>G	intron_variant	ENST00000282226.5	NP_991111.2
FAM151B	XM_011543234.3 linkuse as main transcript	c.73+3000A>G	intron_variant		XP_011541536.1
FAM151B	XM_011543235.3 linkuse as main transcript	c.25+10135A>G	intron_variant		XP_011541537.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
FAM151B	ENST00000282226.5 linkuse as main transcript	c.26-3509A>G	intron_variant	1	NM_205548.3	ENSP00000282226	P1
FAM151B	ENST00000502608.5 linkuse as main transcript	c.26-3509A>G	intron_variant, NMD_transcript_variant	3		ENSP00000427035
FAM151B	ENST00000507084.1 linkuse as main transcript	n.257-1602A>G	intron_variant, non_coding_transcript_variant	3
FAM151B	ENST00000511718.5 linkuse as main transcript	n.395-1602A>G	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.878

AC:

133418

AN:

152028

Hom.:

59213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.731

Gnomad AMI

AF:

0.968

Gnomad AMR

AF:

0.929

Gnomad ASJ

AF:

0.941

Gnomad EAS

AF:

0.923

Gnomad SAS

AF:

0.850

Gnomad FIN

AF:

0.916

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.943

Gnomad OTH

AF:

0.881

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

GnomAD4 genome

AF:

0.877

AC:

133504

AN:

152146

Hom.:

59246

Cov.:

AF XY:

0.877

AC XY:

65209

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.731

Gnomad4 AMR

AF:

0.930

Gnomad4 ASJ

AF:

0.941

Gnomad4 EAS

AF:

0.922

Gnomad4 SAS

AF:

0.850

Gnomad4 FIN

AF:

0.916

Gnomad4 NFE

AF:

0.943

Gnomad4 OTH

AF:

0.880

Alfa

AF:

0.903

Hom.:

9375

Bravo

AF:

0.873

Asia WGS

AF:

0.889

AC:

3091

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

5.1

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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