chr5-29996700-G-A

Position:

• chr5-29996700-G-A

Variant summary

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

The XR_925890.1(LOC105374706):​n.212-1031C>T 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 0.275 in 151,708 control chromosomes in the GnomAD database, including 6,048 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 0.28 (6048 hom., cov: 32)
• Consequence: LOC105374706 XR_925890.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

LOC105374706 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374706	XR_925890.1	n.212-1031C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41685 AN: 151590 Hom.: 6041 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.275 AC: 41721 AN: 151708 Hom.: 6048 Cov.: 32 AF XY: 0.273 AC XY: 20258 AN XY: 74134

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.282

Alfa AF: 0.277 Hom.: 976

Bravo AF: 0.267

Asia WGS AF: 0.0880 AC: 304 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	11
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4342344; hg19: chr5-29996807;