rs28371583

chr1-207321334-A-Gchr1-207321334-A-T

Variant summary

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

The XR_007066838.1(LOC107985251):n.444+352T>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 0.293 in 159,474 control chromosomes in the GnomAD database, including 7,406 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 0.30 (7165 hom., cov: 33)
  • Exomes 𝑓: 0.24 (241 hom.)
• Consequence: LOC107985251 XR_007066838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

Genes affected

LOC107985251 (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 (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985251	XR_007066838.1	n.444+352T>C		intron_variant, non_coding_transcript_variant
LOC107985251	XR_007066837.1	n.444+352T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45008 AN: 152008 Hom.: 7158 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.278

GnomAD4 exome AF: 0.238 AC: 1752 AN: 7348 Hom.: 241 Cov.: 0 AF XY: 0.230 AC XY: 878 AN XY: 3816

Gnomad4 AFR exome AF: 0.418

Gnomad4 AMR exome AF: 0.195

Gnomad4 ASJ exome AF: 0.366

Gnomad4 EAS exome AF: 0.0565

Gnomad4 SAS exome AF: 0.192

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.240

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.296 AC: 45052 AN: 152126 Hom.: 7165 Cov.: 33 AF XY: 0.293 AC XY: 21767 AN XY: 74348

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.276

Alfa AF: 0.305 Hom.: 1206

Bravo AF: 0.296

Asia WGS AF: 0.138 AC: 482 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	4.3
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28371583; hg19: chr1-207494679;