rs748694

Variant names:

• chr17-4646894-C-T
• rs748694
• XR_001752768.2:n.992-56C>T

Variant summary

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

The XR_001752768.2(LOC105371499):​n.992-56C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,144 control chromosomes in the GnomAD database, including 18,631 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 0.48 (18631 hom., cov: 33)
• Consequence: LOC105371499 XR_001752768.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 13 publications found

Genes affected

LOC105371499 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72792 AN: 152028 Hom.: 18617 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.479 AC: 72828 AN: 152144 Hom.: 18631 Cov.: 33 AF XY: 0.487 AC XY: 36244 AN XY: 74378

African (AFR) AF: 0.283 AC: 11732 AN: 41508

American (AMR) AF: 0.547 AC: 8360 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1843 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3370 AN: 5176

South Asian (SAS) AF: 0.617 AC: 2976 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6587 AN: 10574

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36552 AN: 67988

Other (OTH) AF: 0.458 AC: 969 AN: 2116

Alfa AF: 0.515 Hom.: 33901

Bravo AF: 0.463

Asia WGS AF: 0.616 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.80
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs748694; hg19: chr17-4550189;