rs5743404

Positions:

• chr8-6879599-G-A

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):​n.226-5523G>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 0.592 in 151,774 control chromosomes in the GnomAD database, including 27,481 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 0.59 (27481 hom., cov: 30)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-5523G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89757 AN: 151656 Hom.: 27475 Cov.: 30

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.592 AC: 89784 AN: 151774 Hom.: 27481 Cov.: 30 AF XY: 0.597 AC XY: 44289 AN XY: 74166

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.570

Alfa AF: 0.630 Hom.: 41971

Bravo AF: 0.573

Asia WGS AF: 0.527 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743404; hg19: chr8-6737121;