rs17544779

chr17-34793767-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001752848.3(LOC105371742):n.351-31410T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 152,192 control chromosomes in the GnomAD database, including 790 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 0.087 (790 hom., cov: 32)
• Consequence: LOC105371742 XR_001752848.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

Genes affected

LOC105371742 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371742	XR_001752848.3	n.351-31410T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13229 AN: 152074 Hom.: 789 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.0869 AC: 13225 AN: 152192 Hom.: 790 Cov.: 32 AF XY: 0.0894 AC XY: 6651 AN XY: 74434

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0670

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.108 Hom.: 919

Bravo AF: 0.0762

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.8
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17544779; hg19: chr17-33120786;