chr13-97656387-G-A

Position:

• chr13-97656387-G-A

Variant summary

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

The XR_007063845.1(LOC105370324):​n.2614+21404C>T 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 0.208 in 152,182 control chromosomes in the GnomAD database, including 4,220 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 (4220 hom., cov: 32)
• Consequence: LOC105370324 XR_007063845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

Genes affected

LOC105370324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370324	XR_007063845.1	n.2614+21404C>T		intron_variant, non_coding_transcript_variant
LOC105370324	XR_931663.3	n.2670+21404C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31657 AN: 152064 Hom.: 4222 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.208 AC: 31644 AN: 152182 Hom.: 4220 Cov.: 32 AF XY: 0.212 AC XY: 15795 AN XY: 74402

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.224

Alfa AF: 0.249 Hom.: 6709

Bravo AF: 0.204

Asia WGS AF: 0.265 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327918; hg19: chr13-98308641; COSMIC: COSV69618827;