Variant rs2293435 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001029888.3(FAM24A):c.-69G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,982 control chromosomes in the GnomAD database, including 18,679 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 0.49 ( 18677 hom., cov: 31)

Exomes 𝑓: 0.70 ( 2 hom. )

Consequence

FAM24A
NM_001029888.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.886

Variant links:

Genes affected

FAM24A (HGNC:23470): (family with sequence similarity 24 member A) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

FAM24A 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
FAM24A	NM_001029888.3 linkuse as main transcript	c.-69G>A	5_prime_UTR_variant	1/3	ENST00000368894.2
FAM24A	XM_017015638.2 linkuse as main transcript	c.-66G>A	5_prime_UTR_variant	1/3
FAM24A	XM_017015639.2 linkuse as main transcript	c.-3+32G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM24A	ENST00000368894.2 linkuse as main transcript	c.-69G>A		5_prime_UTR_variant	1/3	3	NM_001029888.3	P1

Frequencies

GnomAD3 genomes

AF:

0.489

AC:

74278

AN:

151850

Hom.:

18675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.625

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.490

GnomAD4 exome

AF:

0.700

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.667

GnomAD4 genome

AF:

0.489

AC:

74296

AN:

151972

Hom.:

18677

Cov.:

AF XY:

0.490

AC XY:

36433

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.396

Gnomad4 AMR

AF:

0.468

Gnomad4 ASJ

AF:

0.495

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.462

Gnomad4 FIN

AF:

0.625

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.489

Alfa

AF:

0.495

Hom.:

2367

Bravo

AF:

0.471

Asia WGS

AF:

0.437

AC:

1519

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.92

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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