rs36212413

Variant names:

• chr10-122862834-A-G
• rs36212413
• NM_152644.3:c.-177-7048T>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.-177-7048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0368 in 152,180 control chromosomes in the GnomAD database, including 150 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 0.037 (150 hom., cov: 32)
• Consequence: FAM24B NM_152644.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• Publications: 0 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:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM24B	NM_152644.3	c.-177-7048T>C		intron_variant	Intron 1 of 3	ENST00000368898.8	NP_689857.2
FAM24B	NM_001204364.1	c.-147-7048T>C		intron_variant	Intron 1 of 3		NP_001191293.1
FAM24B	NR_037911.1	n.158-7048T>C		intron_variant	Intron 1 of 2
FAM24B-CUZD1	NR_037915.1	n.158-7048T>C		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM24B	ENST00000368898.8	c.-177-7048T>C		intron_variant	Intron 1 of 3	1	NM_152644.3	ENSP00000357894.3

Frequencies

GnomAD3 genomes AF: 0.0369 AC: 5612 AN: 152062 Hom.: 150 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.0658

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0368 AC: 5605 AN: 152180 Hom.: 150 Cov.: 32 AF XY: 0.0345 AC XY: 2564 AN XY: 74402

African (AFR) AF: 0.0110 AC: 456 AN: 41524

American (AMR) AF: 0.0380 AC: 581 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0658 AC: 228 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4818

European-Finnish (FIN) AF: 0.0255 AC: 271 AN: 10610

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0570 AC: 3877 AN: 67994

Other (OTH) AF: 0.0475 AC: 100 AN: 2106

Alfa AF: 0.0503 Hom.: 274

Bravo AF: 0.0373

Asia WGS AF: 0.00751 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.81
PhyloP100		0.48
Mutation Taster		=100/0	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: rs36212413; hg19: chr10-124622350;