rs4787125

Positions:

• chr16-8078056-A-G

Variant summary

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

The ENST00000670665.1(ENSG00000260289):​n.334+34367T>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 0.354 in 152,098 control chromosomes in the GnomAD database, including 9,880 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 0.35 (9880 hom., cov: 33)
• Consequence: ENST00000670665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371070	XR_001752068.3	n.433+34367T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670665.1	n.334+34367T>C		intron_variant, non_coding_transcript_variant
	ENST00000567103.2	n.301+34367T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000654046.1	n.334+34367T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53783 AN: 151978 Hom.: 9853 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.354 AC: 53861 AN: 152098 Hom.: 9880 Cov.: 33 AF XY: 0.350 AC XY: 26039 AN XY: 74334

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.363

Alfa AF: 0.359 Hom.: 1715

Bravo AF: 0.372

Asia WGS AF: 0.203 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.086
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4787125; hg19: chr16-8128058;