rs320654

Positions:

• chr5-103774079-T-C
• chr5-103774079-T-G

Variant summary

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

The XR_001742831.2(LOC105379107):​n.205-45083T>C 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 0.338 in 152,034 control chromosomes in the GnomAD database, including 9,177 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 0.34 (9177 hom., cov: 33)
• Consequence: LOC105379107 XR_001742831.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

LOC105379107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379107	XR_001742831.2	n.205-45083T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51392 AN: 151916 Hom.: 9170 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.338 AC: 51408 AN: 152034 Hom.: 9177 Cov.: 33 AF XY: 0.335 AC XY: 24910 AN XY: 74326

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.368

Alfa AF: 0.390 Hom.: 23985

Bravo AF: 0.332

Asia WGS AF: 0.252 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.026
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs320654; hg19: chr5-103109780;