rs13401620

Positions:

• chr2-119755557-G-A
• chr2-119755557-G-C

Variant summary

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

The XR_007087215.1(LOC101927764):​n.83+4075C>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 0.258 in 150,614 control chromosomes in the GnomAD database, including 5,088 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 0.26 (5088 hom., cov: 28)
• Consequence: LOC101927764 XR_007087215.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

LOC101927764 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927764	XR_007087215.1	n.83+4075C>T		intron_variant, non_coding_transcript_variant
LOC101927764	XR_001739677.3	n.83+4075C>T		intron_variant, non_coding_transcript_variant
LOC101927764	XR_007087214.1	n.83+4075C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.258 AC: 38800 AN: 150506 Hom.: 5075 Cov.: 28

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.258 AC: 38838 AN: 150614 Hom.: 5088 Cov.: 28 AF XY: 0.259 AC XY: 19045 AN XY: 73480

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.217

Alfa AF: 0.248 Hom.: 3897

Bravo AF: 0.254

Asia WGS AF: 0.276 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13401620; hg19: chr2-120513133;