rs2071495

Positions:

• chr1-23557842-C-G

Variant summary

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

The XR_007065537.1(LOC124903876):​n.282+5747C>G 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 0.13 in 152,704 control chromosomes in the GnomAD database, including 2,112 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 0.13 (2107 hom., cov: 32)
  • Exomes 𝑓: 0.12 (5 hom.)
• Consequence: LOC124903876 XR_007065537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

LOC124903876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903876	XR_007065537.1	n.282+5747C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19839 AN: 152136 Hom.: 2112 Cov.: 32

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.124 AC: 56 AN: 450 Hom.: 5 AF XY: 0.112 AC XY: 31 AN XY: 276

Gnomad4 FIN exome AF: 0.114

Gnomad4 NFE exome AF: 0.313

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.130 AC: 19825 AN: 152254 Hom.: 2107 Cov.: 32 AF XY: 0.131 AC XY: 9715 AN XY: 74432

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.178

Alfa AF: 0.137 Hom.: 240

Bravo AF: 0.136

Asia WGS AF: 0.287 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.5
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: rs2071495; hg19: chr1-23884333;