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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371499	XR_001752768.2	n.992-56C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;