rs1347638

Variant names:

• chr15-34649756-C-T
• rs1347638
• ENST00000720812.1:n.280+4519C>T

Variant summary

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

The ENST00000720812.1(ENSG00000287973):​n.280+4519C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,968 control chromosomes in the GnomAD database, including 8,478 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 0.30 (8478 hom., cov: 32)
• Consequence: ENSG00000287973 ENST00000720812.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 6 publications found

Genes affected

ENSG00000287973 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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
ENSG00000287973	ENST00000720812.1	n.280+4519C>T		intron_variant	Intron 3 of 3
ENSG00000287973	ENST00000720813.1	n.177+23390C>T		intron_variant	Intron 2 of 3
ENSG00000287973	ENST00000720814.1	n.214+23390C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46090 AN: 151848 Hom.: 8470 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.303 AC: 46091 AN: 151968 Hom.: 8478 Cov.: 32 AF XY: 0.301 AC XY: 22351 AN XY: 74268

African (AFR) AF: 0.101 AC: 4174 AN: 41472

American (AMR) AF: 0.284 AC: 4340 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1311 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1915 AN: 5180

South Asian (SAS) AF: 0.343 AC: 1647 AN: 4800

European-Finnish (FIN) AF: 0.300 AC: 3167 AN: 10554

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28334 AN: 67914

Other (OTH) AF: 0.312 AC: 653 AN: 2094

Alfa AF: 0.375 Hom.: 5788

Bravo AF: 0.292

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.84
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs1347638; hg19: chr15-34941957;