rs6989209

Positions:

• chr8-131111367-G-A

Variant summary

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

The XR_928650.3(LOC105375759):​n.614-14922C>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 0.0892 in 152,152 control chromosomes in the GnomAD database, including 627 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 0.089 (627 hom., cov: 32)
• Consequence: LOC105375759 XR_928650.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

Genes affected

LOC105375760 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375760	XR_007061183.1	n.332-18512G>A		intron_variant, non_coding_transcript_variant
LOC105375759	XR_928650.3	n.614-14922C>T		intron_variant, non_coding_transcript_variant
LOC105375760	XR_928653.3	n.194-18512G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0889 AC: 13523 AN: 152032 Hom.: 617 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0892 AC: 13566 AN: 152152 Hom.: 627 Cov.: 32 AF XY: 0.0894 AC XY: 6653 AN XY: 74386

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0982

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0687

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0851 Hom.: 285

Bravo AF: 0.0946

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.023
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6989209; hg19: chr8-132123614;