rs4131099

Positions:

• chr16-51296620-G-A
• chr16-51296620-G-C

Variant summary

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

The ENST00000643626.1(ENSG00000285367):​n.52-14950G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,030 control chromosomes in the GnomAD database, including 11,781 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 0.38 (11781 hom., cov: 32)
• Consequence: ENST00000643626.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643626.1	n.52-14950G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58101 AN: 151912 Hom.: 11768 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.347

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.383 AC: 58156 AN: 152030 Hom.: 11781 Cov.: 32 AF XY: 0.395 AC XY: 29337 AN XY: 74294

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.352

Alfa AF: 0.334 Hom.: 20595

Bravo AF: 0.375

Asia WGS AF: 0.646 AC: 2245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131099; hg19: chr16-51330531;