chr5-73497226-A-G

Variant names:

• chr5-73497226-A-G
• rs347245
• ENST00000607001.3:n.1649T>C

Variant summary

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

The ENST00000607001.3(BTF3-DT):​n.1649T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,124 control chromosomes in the GnomAD database, including 22,535 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 0.52 (22535 hom., cov: 32)
• Consequence: BTF3-DT ENST00000607001.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 6 publications found

Genes affected

BTF3-DT (HGNC:55211): (BTF3 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.722 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
BTF3-DT	ENST00000607001.3	n.1649T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78401 AN: 152006 Hom.: 22535 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.515 AC: 78415 AN: 152124 Hom.: 22535 Cov.: 32 AF XY: 0.518 AC XY: 38497 AN XY: 74358

African (AFR) AF: 0.246 AC: 10213 AN: 41494

American (AMR) AF: 0.639 AC: 9760 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2389 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2430 AN: 5170

South Asian (SAS) AF: 0.743 AC: 3585 AN: 4828

European-Finnish (FIN) AF: 0.519 AC: 5488 AN: 10570

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42579 AN: 67994

Other (OTH) AF: 0.542 AC: 1147 AN: 2116

Alfa AF: 0.598 Hom.: 88635

Bravo AF: 0.511

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.5
DANN	Benign	0.79
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs347245; hg19: chr5-72793051;