rs5899787

chr9-108131271-C-CT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_007061722.1(LOC105376214):n.721-77978_721-77977insA variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.69 in 152,050 control chromosomes in the GnomAD database, including 36,700 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (36700 hom., cov: 0)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.67

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.721-77978_721-77977insA		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.721-77978_721-77977insA		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.721-77978_721-77977insA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104840 AN: 151932 Hom.: 36642 Cov.: 0

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.690 AC: 104958 AN: 152050 Hom.: 36700 Cov.: 0 AF XY: 0.698 AC XY: 51897 AN XY: 74322

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.684

Alfa AF: 0.672 Hom.: 4220

Bravo AF: 0.692

Asia WGS AF: 0.899 AC: 3121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5899787; hg19: chr9-110893551;