19-49255975-G-T

Position:

• chr19-49255975-G-T

Variant summary

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

The variant allele was found at a frequency of 0.496 in 152,132 control chromosomes in the GnomAD database, including 18,901 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 0.50 (18865 hom., cov: 31)
  • Exomes 𝑓: 0.51 (36 hom.)
• Consequence: SLC6A21P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

Genes affected

SLC6A21P (HGNC:31400): (solute carrier family 6 member 21, pseudogene)

LOC107985340 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A21P		n.49255975G>T		intragenic_variant
LOC107985340	XR_001753971.2	n.467-13428G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A21P	ENST00000599458.1	n.91+37C>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75314 AN: 151782 Hom.: 18854 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.509 AC: 118 AN: 232 Hom.: 36 Cov.: 0 AF XY: 0.520 AC XY: 79 AN XY: 152

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.489

Gnomad4 NFE exome AF: 0.483

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.496 AC: 75363 AN: 151900 Hom.: 18865 Cov.: 31 AF XY: 0.503 AC XY: 37334 AN XY: 74226

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.501

Alfa AF: 0.448 Hom.: 3410

Bravo AF: 0.497

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.075
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs352822; hg19: chr19-49759232;