rs17841343

Variant names:

• chr16-49921211-G-A
• rs17841343
• ENST00000563124.1:n.1604C>T

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: ENSG00000261751 ENST00000563124.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

ENSG00000261751 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261751	ENST00000563124.1	n.1604C>T		non_coding_transcript_exon_variant	Exon 2 of 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;