rs6991577

Positions:

• chr8-92867206-C-T

Variant summary

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

The XR_007061007.1(LOC124901978):​n.7707G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0493 in 152,120 control chromosomes in the GnomAD database, including 453 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 0.049 (453 hom., cov: 32)
• Consequence: LOC124901978 XR_007061007.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

Genes affected

LOC124901978 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901978	XR_007061007.1	n.7707G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLJ46284	ENST00000504861.2	n.55+10377G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7486 AN: 152002 Hom.: 451 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0113

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00937

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0493 AC: 7503 AN: 152120 Hom.: 453 Cov.: 32 AF XY: 0.0499 AC XY: 3714 AN XY: 74364

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0113

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.00935

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0317 Hom.: 34

Bravo AF: 0.0529

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6991577; hg19: chr8-93879434;