chr5-56899963-A-G

Position:

• chr5-56899963-A-G

Variant summary

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

The XR_948347.4(LOC105378980):​n.70+34T>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 0.0921 in 152,266 control chromosomes in the GnomAD database, including 652 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 0.092 (652 hom., cov: 32)
  • Exomes 𝑓: 0.065 (0 hom.)
• Consequence: LOC105378980 XR_948347.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

LOC105378980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378980	XR_948347.4	n.70+34T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14018 AN: 152102 Hom.: 651 Cov.: 32

Gnomad AFR AF: 0.0826

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.0652 AC: 3 AN: 46 Hom.: 0 AF XY: 0.0882 AC XY: 3 AN XY: 34

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0921 AC: 14027 AN: 152220 Hom.: 652 Cov.: 32 AF XY: 0.0925 AC XY: 6883 AN XY: 74446

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0929 Hom.: 371

Bravo AF: 0.0940

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12655019; hg19: chr5-56195790;