16-52313907-T-G

Position:

• chr16-52313907-T-G

Variant summary

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

The ENST00000701553.1(ENSG00000289907):​n.332-14041A>C 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 0.312 in 152,028 control chromosomes in the GnomAD database, including 7,931 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 0.31 (7931 hom., cov: 32)
• Consequence: ENST00000701553.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984901	XR_001752185.2	n.451-14041A>C		intron_variant, non_coding_transcript_variant
LOC107984901	XR_001752184.1	n.537-14041A>C		intron_variant, non_coding_transcript_variant
LOC107984901	XR_001752186.1	n.399-14041A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701553.1	n.332-14041A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47294 AN: 151908 Hom.: 7906 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.312 AC: 47361 AN: 152028 Hom.: 7931 Cov.: 32 AF XY: 0.308 AC XY: 22867 AN XY: 74286

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.308

Alfa AF: 0.253 Hom.: 3404

Bravo AF: 0.327

Asia WGS AF: 0.324 AC: 1125 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4784165; hg19: chr16-52347819;