rs45442801

Positions:

• chr8-6870512-G-A
• chr8-6870512-G-C
• chr8-6870512-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000531701.1(GS1-24F4.2):​n.226-14610G>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 0.00273 in 778,678 control chromosomes in the GnomAD database, including 61 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 0.0017 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (52 hom.)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.41

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=-1.01).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0017 (259/151916) while in subpopulation SAS AF= 0.0476 (229/4810). AF 95% confidence interval is 0.0426. There are 9 homozygotes in gnomad4. There are 191 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-14610G>A		intron_variant, non_coding_transcript_variant		3
GS1-24F4.2	ENST00000657010.1	n.1431G>A		non_coding_transcript_exon_variant	5/5
GS1-24F4.2	ENST00000655804.1	n.323-2669G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00170 AC: 258 AN: 151806 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000265

Gnomad OTH AF: 0.00144

GnomAD4 exome AF: 0.00297 AC: 1864 AN: 626762 Hom.: 52 AF XY: 0.00422 AC XY: 1352 AN XY: 320188

Gnomad4 AFR exome AF: 0.000325

Gnomad4 AMR exome AF: 0.000121

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000981

Gnomad4 SAS exome AF: 0.0369

Gnomad4 FIN exome AF: 0.0000342

Gnomad4 NFE exome AF: 0.000190

Gnomad4 OTH exome AF: 0.00280

GnomAD4 genome AF: 0.00170 AC: 259 AN: 151916 Hom.: 9 Cov.: 32 AF XY: 0.00257 AC XY: 191 AN XY: 74220

Gnomad4 AFR AF: 0.000145

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.0000694 Hom.: 0

Bravo AF: 0.000502

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
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: rs45442801; hg19: chr8-6728034;