rs987858

chr3-16049413-T-A

Variant summary

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

The ENST00000702609.1(ENSG00000287042):n.197-87978T>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 0.263 in 152,160 control chromosomes in the GnomAD database, including 5,482 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 0.26 (5482 hom., cov: 33)
• Consequence: ENST00000702609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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
	ENST00000702609.1	n.197-87978T>A		intron_variant, non_coding_transcript_variant
	ENST00000691919.2	n.240-87978T>A		intron_variant, non_coding_transcript_variant
	ENST00000702385.1	n.230-87978T>A		intron_variant, non_coding_transcript_variant
	ENST00000702645.1	n.549-87978T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40057 AN: 152042 Hom.: 5480 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.263 AC: 40075 AN: 152160 Hom.: 5482 Cov.: 33 AF XY: 0.255 AC XY: 18999 AN XY: 74396

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.283

Alfa AF: 0.259 Hom.: 636

Bravo AF: 0.272

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987858; hg19: chr3-16090920;