NM_001029888.3:c.-69G>A

Variant names:

• chr10-122910753-G-A
• rs2293435
• NM_001029888.3:c.-69G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029888.3(FAM24A):​c.-69G>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 0.489 in 151,982 control chromosomes in the GnomAD database, including 18,679 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 0.49 (18677 hom., cov: 31)
  • Exomes 𝑓: 0.70 (2 hom.)
• Consequence: FAM24A NM_001029888.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 9 publications found

Genes affected

FAM24A (HGNC:23470): (family with sequence similarity 24 member A) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001029888.3. 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
	FAM24A	NM_001029888.3	MANE Select	c.-69G>A		5_prime_UTR	Exon 1 of 3	NP_001025059.1	A6NFZ4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM24A	ENST00000368894.2	TSL:3 MANE Select	c.-69G>A		5_prime_UTR	Exon 1 of 3	ENSP00000357889.1	A6NFZ4

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74278 AN: 151850 Hom.: 18675 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.490

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.489 AC: 74296 AN: 151972 Hom.: 18677 Cov.: 31 AF XY: 0.490 AC XY: 36433 AN XY: 74280

African (AFR) AF: 0.396 AC: 16419 AN: 41436

American (AMR) AF: 0.468 AC: 7163 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2186 AN: 5150

South Asian (SAS) AF: 0.462 AC: 2226 AN: 4822

European-Finnish (FIN) AF: 0.625 AC: 6587 AN: 10544

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36199 AN: 67954

Other (OTH) AF: 0.489 AC: 1026 AN: 2098

Alfa AF: 0.491 Hom.: 2428

Bravo AF: 0.471

Asia WGS AF: 0.437 AC: 1519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.42
PhyloP100		-0.89
PromoterAI		-0.0040	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2293435; hg19: chr10-124670269;