rs4843869

chr16-85941535-G-A

Variant summary

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

The ENST00000646214.1(ENSG00000285163):n.78-3881G>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 0.175 in 152,122 control chromosomes in the GnomAD database, including 2,734 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 0.18 (2734 hom., cov: 31)
• Consequence: ENST00000646214.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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
	ENST00000646214.1	n.78-3881G>A		intron_variant, non_coding_transcript_variant
	ENST00000645383.1	n.394-3881G>A		intron_variant, non_coding_transcript_variant
	ENST00000646986.1	n.716-3881G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26624 AN: 152004 Hom.: 2733 Cov.: 31

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.175 AC: 26638 AN: 152122 Hom.: 2734 Cov.: 31 AF XY: 0.175 AC XY: 12985 AN XY: 74354

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0914

Gnomad4 EAS AF: 0.0878

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.155

Alfa AF: 0.194 Hom.: 707

Bravo AF: 0.167

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.1
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4843869; hg19: chr16-85975141;