5-56899963-A-G

Variant names:

• chr5-56899963-A-G
• rs12655019
• XR_948347.4:n.70+34T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_948347.4(LOC105378980):​n.70+34T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 14 publications found

Genes affected

LOC105378980 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453721.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225230	ENST00000453721.1	TSL:3	n.*78T>C		downstream_gene	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.136 AC: 3 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.0825 AC: 3427 AN: 41542

American (AMR) AF: 0.0896 AC: 1371 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3472

East Asian (EAS) AF: 0.145 AC: 748 AN: 5168

South Asian (SAS) AF: 0.100 AC: 483 AN: 4826

European-Finnish (FIN) AF: 0.0831 AC: 881 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6464 AN: 67992

Other (OTH) AF: 0.105 AC: 221 AN: 2114

Alfa AF: 0.0941 Hom.: 1266

Bravo AF: 0.0940

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.39
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs12655019; hg19: chr5-56195790;