rs11668247

Positions:

• chr19-43690210-C-T

Variant summary

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

The NR_172891.1(LOC105372412):​n.826+79C>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 0.344 in 151,982 control chromosomes in the GnomAD database, including 9,310 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 0.34 (9309 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: LOC105372412 NR_172891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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 (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372412	NR_172891.1	n.826+79C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636801.1	n.160+49C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52234 AN: 151854 Hom.: 9307 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.377

GnomAD4 exome AF: 0.500 AC: 5 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.344 AC: 52260 AN: 151972 Hom.: 9309 Cov.: 31 AF XY: 0.342 AC XY: 25437 AN XY: 74272

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.377

Alfa AF: 0.370 Hom.: 5826

Bravo AF: 0.355

Asia WGS AF: 0.416 AC: 1446 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	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11668247; hg19: chr19-44194362;