rs6871834

chr5-40480085-G-A

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, non coding transcript 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: ENST00000648975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648975.1	n.2421-1993C>T		intron_variant, non_coding_transcript_variant
	ENST00000649444.1	n.120-6291G>A		intron_variant, non_coding_transcript_variant
	ENST00000649894.1	n.119+16405G>A		intron_variant, non_coding_transcript_variant

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;