rs3128982

Variant names:

• chr6-31449414-A-G
• rs3128982
• ENST00000673857.1:n.63-13709A>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-13709A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,532 control chromosomes in the GnomAD database, including 4,306 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 0.21 (4306 hom., cov: 30)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.63-13709A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31830 AN: 151414 Hom.: 4305 Cov.: 30

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.210 AC: 31840 AN: 151532 Hom.: 4306 Cov.: 30 AF XY: 0.203 AC XY: 14997 AN XY: 74040

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.182

Alfa AF: 0.277 Hom.: 9088

Bravo AF: 0.197

Asia WGS AF: 0.0880 AC: 310 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3128982; hg19: chr6-31417191;