13-97686601-C-G

Variant names:

• chr13-97686601-C-G
• rs4771280
• XR_007063845.1:n.2442-8638G>C

Variant summary

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

The XR_007063845.1(LOC105370324):​n.2442-8638G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,004 control chromosomes in the GnomAD database, including 3,981 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 0.21 (3981 hom., cov: 32)
• Consequence: LOC105370324 XR_007063845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 4 publications found

Genes affected

LOC105370324 (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 (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32472 AN: 151886 Hom.: 3981 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.214 AC: 32483 AN: 152004 Hom.: 3981 Cov.: 32 AF XY: 0.212 AC XY: 15726 AN XY: 74276

African (AFR) AF: 0.107 AC: 4426 AN: 41466

American (AMR) AF: 0.160 AC: 2446 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 595 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1190 AN: 5160

South Asian (SAS) AF: 0.194 AC: 933 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3232 AN: 10516

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19024 AN: 67972

Other (OTH) AF: 0.195 AC: 411 AN: 2110

Alfa AF: 0.142 Hom.: 295

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4771280; hg19: chr13-98338855;