rs36212413

Positions:

• chr10-122862834-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.-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

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=-0.89).
• 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/exons	MANE	Protein	UniProt
FAM24B	NM_152644.3	c.-177-7048T>C		intron_variant		ENST00000368898.8	NP_689857.2
FAM24B-CUZD1	NR_037915.1	n.158-7048T>C		intron_variant, non_coding_transcript_variant
FAM24B	NM_001204364.1	c.-147-7048T>C		intron_variant			NP_001191293.1
FAM24B	NR_037911.1	n.158-7048T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM24B	ENST00000368898.8	c.-177-7048T>C		intron_variant		1	NM_152644.3	ENSP00000357894	P1
FAM24B	ENST00000368896.1	c.-147-7048T>C		intron_variant		2		ENSP00000357892	P1
FAM24B	ENST00000462859.5	n.158-7048T>C		intron_variant, non_coding_transcript_variant		2
FAM24B	ENST00000489000.1	n.98-7048T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0380

Gnomad4 ASJ AF: 0.0658

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.0255

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0475

Alfa AF: 0.0494 Hom.: 43

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

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: rs36212413; hg19: chr10-124622350;