10-122879507-C-T

Position:

• chr10-122879507-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_152644.3(FAM24B):​c.-200G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00641 in 152,360 control chromosomes in the GnomAD database, including 8 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 0.0064 (8 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FAM24B NM_152644.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM24B	NM_152644.3	c.-200G>A		5_prime_UTR_variant	1/4	ENST00000368898.8
FAM24B-CUZD1	NR_037915.1	n.135G>A		non_coding_transcript_exon_variant	1/11
FAM24B	NM_001204364.1	c.-170G>A		5_prime_UTR_variant	1/4
FAM24B	NR_037911.1	n.135G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM24B	ENST00000368898.8	c.-200G>A		5_prime_UTR_variant	1/4	1	NM_152644.3	P1
FAM24B	ENST00000368896.1	c.-170G>A		5_prime_UTR_variant	1/4	2		P1
FAM24B	ENST00000462859.5	n.135G>A		non_coding_transcript_exon_variant	1/3	2
FAM24B	ENST00000489000.1	n.75G>A		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.00636 AC: 968 AN: 152242 Hom.: 8 Cov.: 33

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00242

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000558

Gnomad OTH AF: 0.00239

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 254 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 186

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00641 AC: 977 AN: 152360 Hom.: 8 Cov.: 33 AF XY: 0.00666 AC XY: 496 AN XY: 74516

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.00242

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.0125

Gnomad4 SAS AF: 0.000828

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000559

Gnomad4 OTH AF: 0.00378

Alfa AF: 0.000137 Hom.: 0

Bravo AF: 0.00743

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	9.8
DANN	Benign	0.97

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: rs36212727; hg19: chr10-124639023;