rs3859501

Positions:

• chr19-53788157-A-C
• chr19-53788157-A-T

Variant summary

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

The ENST00000595160.1(ENSG00000269877):​n.13T>G 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 0.452 in 255,420 control chromosomes in the GnomAD database, including 27,577 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 0.44 (15486 hom., cov: 30)
  • Exomes 𝑓: 0.47 (12091 hom.)
• Consequence: ENST00000595160.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904767	XR_007067336.1	n.69T>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000595160.1	n.13T>G		non_coding_transcript_exon_variant	1/2	3
	ENST00000597420.2	n.90-440A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66411 AN: 151662 Hom.: 15483 Cov.: 30

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.500

GnomAD4 exome AF: 0.474 AC: 49136 AN: 103640 Hom.: 12091 Cov.: 0 AF XY: 0.470 AC XY: 26500 AN XY: 56422

Gnomad4 AFR exome AF: 0.263

Gnomad4 AMR exome AF: 0.448

Gnomad4 ASJ exome AF: 0.540

Gnomad4 EAS exome AF: 0.532

Gnomad4 SAS exome AF: 0.402

Gnomad4 FIN exome AF: 0.456

Gnomad4 NFE exome AF: 0.507

Gnomad4 OTH exome AF: 0.490

GnomAD4 genome AF: 0.438 AC: 66436 AN: 151780 Hom.: 15486 Cov.: 30 AF XY: 0.433 AC XY: 32103 AN XY: 74186

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.503

Alfa AF: 0.508 Hom.: 25689

Bravo AF: 0.439

Asia WGS AF: 0.415 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3859501; hg19: chr19-54291411;