rs2627282

Positions:

• chr8-2923434-G-A

Variant summary

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

The NR_168443.1(LOC105377785):​n.1172-85134G>A 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 0.244 in 152,124 control chromosomes in the GnomAD database, including 5,691 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 0.24 (5691 hom., cov: 33)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

Genes affected

LOC105377785 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377785	NR_168443.1	n.1172-85134G>A		intron_variant, non_coding_transcript_variant
LOC124901871	XR_007060785.1	n.75+128C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37124 AN: 152006 Hom.: 5693 Cov.: 33

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.244 AC: 37117 AN: 152124 Hom.: 5691 Cov.: 33 AF XY: 0.239 AC XY: 17805 AN XY: 74352

Gnomad4 AFR AF: 0.0845

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.269

Alfa AF: 0.302 Hom.: 1528

Bravo AF: 0.231

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2627282; hg19: chr8-2780956;