rs7164726

chr15-59423467-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560394.5(FAM81A):c.-78+21109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,090 control chromosomes in the GnomAD database, including 4,216 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 (4216 hom., cov: 32)
• Consequence: FAM81A ENST00000560394.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM81A	XM_011521248.3	c.-22+21109C>T		intron_variant
FAM81A	XM_047432170.1	c.-78+21109C>T		intron_variant
FAM81A	XM_047432171.1	c.-78+21109C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM81A	ENST00000558348.5	c.-78+21109C>T		intron_variant		4
FAM81A	ENST00000560394.5	c.-78+21109C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31158 AN: 151972 Hom.: 4212 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.205 AC: 31194 AN: 152090 Hom.: 4216 Cov.: 32 AF XY: 0.210 AC XY: 15628 AN XY: 74324

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.201

Alfa AF: 0.140 Hom.: 1023

Bravo AF: 0.210

Asia WGS AF: 0.376 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7164726; hg19: chr15-59715666;