rs4238186

Positions:

• chr13-19116696-G-A
• chr13-19116696-G-T

Variant summary

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

The NR_146902.1(LOC107984132):​n.305+1283C>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 0.257 in 152,102 control chromosomes in the GnomAD database, including 5,831 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 (5831 hom., cov: 33)
• Consequence: LOC107984132 NR_146902.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.954

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984132	NR_146902.1	n.305+1283C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657315.1	n.337+1283C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39049 AN: 151984 Hom.: 5816 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.257 AC: 39102 AN: 152102 Hom.: 5831 Cov.: 33 AF XY: 0.254 AC XY: 18902 AN XY: 74336

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.283

Alfa AF: 0.205 Hom.: 4435

Bravo AF: 0.267

Asia WGS AF: 0.281 AC: 980 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	6.5
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4238186; hg19: chr13-19690836;