rs141756767

Variant names:

• chr10-122850432-G-A
• rs141756767
• NM_152644.3:c.84C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-122850432-G-A
• chr10-122850432-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_152644.3(FAM24B):​c.84C>T​(p.Asn28Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000586 in 1,613,484 control chromosomes in the GnomAD database, including 3 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 0.0032 (3 hom., cov: 32)
  • Exomes 𝑓: 0.00031 (0 hom.)
• Consequence: FAM24B NM_152644.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM24B	NM_152644.3	c.84C>T	p.Asn28Asn	synonymous_variant	Exon 3 of 4	ENST00000368898.8	NP_689857.2
FAM24B	NM_001204364.1	c.84C>T	p.Asn28Asn	synonymous_variant	Exon 3 of 4		NP_001191293.1
FAM24B	NR_037911.1	n.300-993C>T		intron_variant	Intron 2 of 2
FAM24B-CUZD1	NR_037915.1	n.300-4212C>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM24B	ENST00000368898.8	c.84C>T	p.Asn28Asn	synonymous_variant	Exon 3 of 4	1	NM_152644.3	ENSP00000357894.3
ENSG00000286088	ENST00000368904.6	n.-377-4212C>T		intron_variant	Intron 1 of 9	1		ENSP00000357900.2

Frequencies

GnomAD3 genomes AF: 0.00320 AC: 487 AN: 152074 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000525

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.000835 AC: 210 AN: 251398 Hom.: 1 AF XY: 0.000633 AC XY: 86 AN XY: 135866

Gnomad AFR exome AF: 0.0113

Gnomad AMR exome AF: 0.000173

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.000425

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000352

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000313 AC: 458 AN: 1461292 Hom.: 0 Cov.: 30 AF XY: 0.000281 AC XY: 204 AN XY: 726996

Gnomad4 AFR exome AF: 0.0106

Gnomad4 AMR exome AF: 0.000268

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.000464

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000234

Gnomad4 OTH exome AF: 0.000381

GnomAD4 genome AF: 0.00321 AC: 488 AN: 152192 Hom.: 3 Cov.: 32 AF XY: 0.00300 AC XY: 223 AN XY: 74404

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.000524

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000588

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00168 Hom.: 0

Bravo AF: 0.00355

EpiCase AF: 0.000218

EpiControl AF: 0.0000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.28		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.28		Position offset: -8

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs141756767; hg19: chr10-124609948; COSMIC: COSV59026502; COSMIC: COSV59026502;