rs6888952

Positions:

• chr5-40412364-A-G

Variant summary

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

The ENST00000691408.1(ENSG00000283286):​n.186+968A>G 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 0.57 in 151,912 control chromosomes in the GnomAD database, including 25,423 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 0.57 (25423 hom., cov: 31)
• Consequence: ENST00000691408.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 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
	ENST00000691408.1	n.186+968A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86582 AN: 151794 Hom.: 25408 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.570 AC: 86641 AN: 151912 Hom.: 25423 Cov.: 31 AF XY: 0.563 AC XY: 41775 AN XY: 74244

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.580

Alfa AF: 0.594 Hom.: 3341

Bravo AF: 0.564

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6888952; hg19: chr5-40412466;