rs1824780

Variant names:

• chr5-100308375-A-C
• rs1824780
• ENST00000720529.1:n.644+497T>G

Variant summary

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

The ENST00000720529.1(FAM174A-DT):​n.644+497T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,918 control chromosomes in the GnomAD database, including 4,407 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 0.23 (4407 hom., cov: 32)
• Consequence: FAM174A-DT ENST00000720529.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 7 publications found

Genes affected

FAM174A-DT (HGNC:55584): (FAM174A divergent transcript)

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 (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM174A-DT	ENST00000720529.1	n.644+497T>G		intron_variant	Intron 6 of 7
FAM174A-DT	ENST00000720532.1	n.336+497T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35190 AN: 151800 Hom.: 4398 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.0184

Gnomad SAS AF: 0.0958

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.232 AC: 35237 AN: 151918 Hom.: 4407 Cov.: 32 AF XY: 0.228 AC XY: 16965 AN XY: 74250

African (AFR) AF: 0.208 AC: 8649 AN: 41498

American (AMR) AF: 0.341 AC: 5177 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3466

East Asian (EAS) AF: 0.0185 AC: 95 AN: 5146

South Asian (SAS) AF: 0.0963 AC: 464 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1993 AN: 10586

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16969 AN: 67890

Other (OTH) AF: 0.266 AC: 561 AN: 2106

Alfa AF: 0.258 Hom.: 922

Bravo AF: 0.247

Asia WGS AF: 0.0840 AC: 295 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs1824780; hg19: chr5-99644079;