rs36212728

Variant names:

• chr10-122879577-A-G
• rs36212728
• NM_152644.3:c.-270T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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:):

C10orf88B (HGNC:44080): (C10orf88B (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152644.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM24B	NM_152644.3	MANE Select	c.-270T>C		5_prime_UTR	Exon 1 of 4	NP_689857.2	Q8N5W8
	FAM24B	NM_001204364.1		c.-240T>C		5_prime_UTR	Exon 1 of 4	NP_001191293.1	Q8N5W8
	FAM24B	NR_037911.1		n.65T>C		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM24B	ENST00000368898.8	TSL:1 MANE Select	c.-270T>C		5_prime_UTR	Exon 1 of 4	ENSP00000357894.3	Q8N5W8
	FAM24B	ENST00000368896.1	TSL:2	c.-240T>C		5_prime_UTR	Exon 1 of 4	ENSP00000357892.1	Q8N5W8
	FAM24B	ENST00000868557.1		c.-5444T>C		5_prime_UTR	Exon 1 of 4	ENSP00000538616.1

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

African (AFR) AF: 0.143 AC: 2 AN: 14

American (AMR) AF: 0.00 AC: 0 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 1 AN: 6

East Asian (EAS) AF: 0.00 AC: 0 AN: 36

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 18

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 322

Other (OTH) AF: 0.0294 AC: 1 AN: 34

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

African (AFR) AF: 0.0830 AC: 3451 AN: 41582

American (AMR) AF: 0.00993 AC: 152 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3472

East Asian (EAS) AF: 0.0126 AC: 65 AN: 5176

South Asian (SAS) AF: 0.00124 AC: 6 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000956 AC: 65 AN: 68022

Other (OTH) AF: 0.0118 AC: 25 AN: 2116

Alfa AF: 0.0214 Hom.: 7

Bravo AF: 0.0296

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.0
DANN	Benign	0.50
PhyloP100		-0.33
PromoterAI		-0.073	Neutral
Mutation Taster		=300/0	polymorphism

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

Other links and lift over

dbSNP: rs36212728; hg19: chr10-124639093;