rs36212728

Positions:

• chr10-122879577-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152644.3(FAM24B):​c.-270T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0257 in 152,792 control chromosomes in the GnomAD database, including 152 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 0.026 (152 hom., cov: 33)
  • Exomes 𝑓: 0.0089 (0 hom.)
• Consequence: FAM24B NM_152644.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

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]

FAM24B-CUZD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM24B	NM_152644.3	c.-270T>C		5_prime_UTR_variant	1/4	ENST00000368898.8	NP_689857.2
FAM24B-CUZD1	NR_037915.1	n.65T>C		non_coding_transcript_exon_variant	1/11
FAM24B	NM_001204364.1	c.-240T>C		5_prime_UTR_variant	1/4		NP_001191293.1
FAM24B	NR_037911.1	n.65T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM24B	ENST00000368898.8	c.-270T>C		5_prime_UTR_variant	1/4	1	NM_152644.3	ENSP00000357894	P1
FAM24B	ENST00000368896.1	c.-240T>C		5_prime_UTR_variant	1/4	2		ENSP00000357892	P1
FAM24B	ENST00000462859.5	n.65T>C		non_coding_transcript_exon_variant	1/3	2
FAM24B	ENST00000489000.1	n.5T>C		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3908 AN: 152226 Hom.: 149 Cov.: 33

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00994

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000955

Gnomad OTH AF: 0.0105

GnomAD4 exome AF: 0.00889 AC: 4 AN: 450 Hom.: 0 Cov.: 0 AF XY: 0.00680 AC XY: 2 AN XY: 294

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.167

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: 0.0294

GnomAD4 genome AF: 0.0258 AC: 3925 AN: 152342 Hom.: 152 Cov.: 33 AF XY: 0.0260 AC XY: 1940 AN XY: 74508

Gnomad4 AFR AF: 0.0830

Gnomad4 AMR AF: 0.00993

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000956

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.0182 Hom.: 4

Bravo AF: 0.0296

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.0
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs36212728; hg19: chr10-124639093;