rs17841343

chr16-49921211-G-A

Variant summary

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

The ENST00000563124.1(ENSG00000261751):n.1604C>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 0.339 in 152,080 control chromosomes in the GnomAD database, including 9,505 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 (9504 hom., cov: 32)
  • Exomes 𝑓: 0.27 (1 hom.)
• Consequence: ENST00000563124.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000563124.1	n.1604C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51460 AN: 151940 Hom.: 9463 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.342

GnomAD4 exome AF: 0.273 AC: 6 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 4 AN XY: 12

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.339 AC: 51555 AN: 152058 Hom.: 9504 Cov.: 32 AF XY: 0.341 AC XY: 25328 AN XY: 74314

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.342

Alfa AF: 0.292 Hom.: 2807

Bravo AF: 0.339

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17841343; hg19: chr16-49955122;