rs141194908

Variant names:

• chr10-122850503-C-A
• NM_152644.3:c.13G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-122850503-C-A
• chr10-122850503-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_152644.3(FAM24B):​c.13G>T​(p.Ala5Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A5T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: FAM24B NM_152644.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

Genes affected

FAM24B (HGNC:23475): (family with sequence similarity 24 member B) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286088 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM24B	NM_152644.3	c.13G>T	p.Ala5Ser	missense_variant	Exon 3 of 4	ENST00000368898.8	NP_689857.2
FAM24B	NM_001204364.1	c.13G>T	p.Ala5Ser	missense_variant	Exon 3 of 4		NP_001191293.1
FAM24B	NR_037911.1	n.300-1064G>T		intron_variant	Intron 2 of 2
FAM24B-CUZD1	NR_037915.1	n.300-4283G>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM24B	ENST00000368898.8	c.13G>T	p.Ala5Ser	missense_variant	Exon 3 of 4	1	NM_152644.3	ENSP00000357894.3
ENSG00000286088	ENST00000368904.6	n.-377-4283G>T		intron_variant	Intron 1 of 9	1		ENSP00000357900.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1460892 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 726840

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.2
DANN	Benign	0.87
DEOGEN2	Benign	0.025	T;T
Eigen	Benign	-0.53
Eigen_PC	Benign	-0.72
FATHMM_MKL	Benign	0.045	N
LIST_S2	Benign	0.28	.;T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.091	T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.40	N;N
REVEL	Benign	0.033
Sift	Benign	0.18	T;T
Sift4G	Uncertain	0.055	T;T
Polyphen		0.87	P;P
Vest4		0.082
MutPred		0.36		Gain of glycosylation at A5 (P = 7e-04);Gain of glycosylation at A5 (P = 7e-04);
MVP		0.095
MPC		0.23
ClinPred		0.21	T
GERP RS		0.97
Varity_R		0.028
gMVP		0.074

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.23		Position offset: 47

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-124610019;