chr5-100302184-A-C

Variant names:

• chr5-100302184-A-C
• rs1973172
• ENST00000720529.1:n.644+6688T>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+6688T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,304 control chromosomes in the GnomAD database, including 4,906 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 0.25 (4906 hom., cov: 30)
• Consequence: FAM174A-DT ENST00000720529.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 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+6688T>G		intron_variant	Intron 6 of 7
FAM174A-DT	ENST00000720532.1	n.336+6688T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37154 AN: 151184 Hom.: 4895 Cov.: 30

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.246 AC: 37209 AN: 151304 Hom.: 4906 Cov.: 30 AF XY: 0.243 AC XY: 17958 AN XY: 73950

African (AFR) AF: 0.230 AC: 9488 AN: 41304

American (AMR) AF: 0.350 AC: 5294 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1161 AN: 3456

East Asian (EAS) AF: 0.0195 AC: 100 AN: 5120

South Asian (SAS) AF: 0.0975 AC: 468 AN: 4798

European-Finnish (FIN) AF: 0.217 AC: 2291 AN: 10544

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17527 AN: 67668

Other (OTH) AF: 0.287 AC: 601 AN: 2094

Alfa AF: 0.257 Hom.: 20032

Bravo AF: 0.262

Asia WGS AF: 0.0890 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.81
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1973172; hg19: chr5-99637888;