rs6991577

Variant names:

• chr8-92867206-C-T
• rs6991577
• XR_007061007.1:n.7707G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

LOC124901978 (HGNC:):

ENSG00000253577 (HGNC:58428):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124901978	XR_007061007.1	n.7707G>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLJ46284	ENST00000504861.3	n.58+10377G>A		intron_variant	Intron 1 of 3	2
FLJ46284	ENST00000744035.1	n.69+10341G>A		intron_variant	Intron 1 of 2
FLJ46284	ENST00000744036.1	n.91+10341G>A		intron_variant	Intron 1 of 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

African (AFR) AF: 0.140 AC: 5818 AN: 41470

American (AMR) AF: 0.0226 AC: 346 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 39 AN: 3466

East Asian (EAS) AF: 0.0417 AC: 215 AN: 5154

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4826

European-Finnish (FIN) AF: 0.0286 AC: 303 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00935 AC: 636 AN: 67998

Other (OTH) AF: 0.0336 AC: 71 AN: 2114

Alfa AF: 0.0172 Hom.: 121

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6991577; hg19: chr8-93879434;