rs6871834

Variant names:

• chr5-40480085-G-A
• rs6871834
• ENST00000648975.1:n.2421-1993C>T

Variant summary

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

The ENST00000648975.1(ENSG00000285616):​n.2421-1993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,930 control chromosomes in the GnomAD database, including 26,584 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 0.58 (26584 hom., cov: 31)
• Consequence: ENSG00000285616 ENST00000648975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

Genes affected

ENSG00000285616 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 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
ENSG00000285616	ENST00000648975.1	n.2421-1993C>T		intron_variant	Intron 1 of 2
ENSG00000285552	ENST00000649444.1	n.120-6291G>A		intron_variant	Intron 1 of 2
ENSG00000285552	ENST00000649894.1	n.119+16405G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88281 AN: 151812 Hom.: 26571 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.581 AC: 88329 AN: 151930 Hom.: 26584 Cov.: 31 AF XY: 0.575 AC XY: 42668 AN XY: 74250

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.603

Alfa AF: 0.635 Hom.: 7641

Bravo AF: 0.578

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6871834; hg19: chr5-40480187;