rs4251416

chr17-30238543-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_001752824.2(LOC105371720):n.634A>G 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 0.0134 in 151,924 control chromosomes in the GnomAD database, including 21 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 0.013 (21 hom., cov: 32)
• Consequence: LOC105371720 XR_001752824.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

Genes affected

LOC105371720 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0134 (2035/151924) while in subpopulation NFE AF= 0.0229 (1554/67910). AF 95% confidence interval is 0.0219. There are 21 homozygotes in gnomad4. There are 933 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371720	XR_001752824.2	n.634A>G		non_coding_transcript_exon_variant	3/4
LOC105371720	XR_007065695.1	n.498A>G		non_coding_transcript_exon_variant	2/3
LOC105371720	XR_007065696.1	n.498A>G		non_coding_transcript_exon_variant	2/3
LOC105371720	XR_007065698.1	n.498A>G		non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0134 AC: 2035 AN: 151806 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.00375

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00649

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00500

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0229

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0134 AC: 2035 AN: 151924 Hom.: 21 Cov.: 32 AF XY: 0.0126 AC XY: 933 AN XY: 74276

Gnomad4 AFR AF: 0.00374

Gnomad4 AMR AF: 0.00648

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00501

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.0229

Gnomad4 OTH AF: 0.0119

Alfa AF: 0.0197 Hom.: 3

Bravo AF: 0.0126

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.90
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4251416; hg19: chr17-28565561; COSMIC: COSV55566301;