rs7164726

Variant names:

• chr15-59423467-C-T
• rs7164726
• ENST00000867392.1:c.-78+21109C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 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+21109C>T		intron	N/A	ENSP00000537451.1
	FAM81A	ENST00000943843.1		c.-78+21109C>T		intron	N/A	ENSP00000613902.1
	FAM81A	ENST00000560394.5	TSL:4	c.-78+21109C>T		intron	N/A	ENSP00000452962.1	H0YKW2

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

African (AFR) AF: 0.354 AC: 14685 AN: 41460

American (AMR) AF: 0.168 AC: 2560 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2180 AN: 5164

South Asian (SAS) AF: 0.337 AC: 1620 AN: 4810

European-Finnish (FIN) AF: 0.149 AC: 1576 AN: 10580

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7269 AN: 68012

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.150 Hom.: 4931

Bravo AF: 0.210

Asia WGS AF: 0.376 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.72
PhyloP100		0.010

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7164726;

hg19: chr15-59715666;