rs6996964

chr8-19766400-C-T

Variant summary

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

The XR_001745821.2(LOC107986920):n.455-4147G>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 0.137 in 151,954 control chromosomes in the GnomAD database, including 2,355 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 0.14 (2355 hom., cov: 30)
• Consequence: LOC107986920 XR_001745821.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

LOC107986920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986920	XR_001745821.2	n.455-4147G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20834 AN: 151836 Hom.: 2339 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0539

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.137 AC: 20885 AN: 151954 Hom.: 2355 Cov.: 30 AF XY: 0.133 AC XY: 9886 AN XY: 74264

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.0908

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.0552

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0822 Hom.: 1321

Bravo AF: 0.148

Asia WGS AF: 0.0570 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.13
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6996964; hg19: chr8-19623911;