chr19-49255975-G-T

Variant names:

• chr19-49255975-G-T
• rs352822
• ENST00000751527.1:n.89G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751527.1(ENSG00000297879):​n.89G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000297879 ENST00000751527.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 6 publications found

Genes affected

ENSG00000297879 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751527.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297879	ENST00000751527.1		n.89G>T		non_coding_transcript_exon	Exon 2 of 3
	SLC6A21P	ENST00000599458.1	TSL:6	n.91+37C>A		intron	N/A
	ENSG00000297851	ENST00000751404.1		n.345+38C>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.489 AC: 46 AN: 94

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.483 AC: 57 AN: 118

Other (OTH) AF: 0.750 AC: 9 AN: 12

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

African (AFR) AF: 0.434 AC: 18001 AN: 41436

American (AMR) AF: 0.570 AC: 8684 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1924 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3228 AN: 5146

South Asian (SAS) AF: 0.590 AC: 2837 AN: 4810

European-Finnish (FIN) AF: 0.511 AC: 5398 AN: 10558

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.494 AC: 33548 AN: 67928

Other (OTH) AF: 0.501 AC: 1055 AN: 2104

Alfa AF: 0.447 Hom.: 3483

Bravo AF: 0.497

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.075
DANN	Benign	0.60
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs352822; hg19: chr19-49759232;