chr15-59426970-A-G

Variant names:

• chr15-59426970-A-G
• rs28890483
• ENST00000867392.1:c.-78+24612A>G

Variant summary

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

The ENST00000560394.5(FAM81A):​c.-78+24612A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,178 control chromosomes in the GnomAD database, including 4,548 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 0.21 (4548 hom., cov: 33)
• Consequence: FAM81A ENST00000560394.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 5 publications found

Genes affected

FAM81A (HGNC:28379): (family with sequence similarity 81 member A)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560394.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM81A	ENST00000867392.1		c.-78+24612A>G		intron	N/A	ENSP00000537451.1
	FAM81A	ENST00000943843.1		c.-78+24612A>G		intron	N/A	ENSP00000613902.1
	FAM81A	ENST00000560394.5	TSL:4	c.-78+24612A>G		intron	N/A	ENSP00000452962.1	H0YKW2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32294 AN: 152060 Hom.: 4531 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.213 AC: 32347 AN: 152178 Hom.: 4548 Cov.: 33 AF XY: 0.220 AC XY: 16370 AN XY: 74410

African (AFR) AF: 0.347 AC: 14376 AN: 41482

American (AMR) AF: 0.299 AC: 4568 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3468

East Asian (EAS) AF: 0.429 AC: 2225 AN: 5184

South Asian (SAS) AF: 0.351 AC: 1694 AN: 4824

European-Finnish (FIN) AF: 0.128 AC: 1353 AN: 10600

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6875 AN: 68022

Other (OTH) AF: 0.213 AC: 449 AN: 2108

Alfa AF: 0.154 Hom.: 5168

Bravo AF: 0.228

Asia WGS AF: 0.383 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.65
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs28890483; hg19: chr15-59719169;