rs6992112

Positions:

• chr8-16787646-T-A
• chr8-16787646-T-G

Variant summary

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

The ENST00000521411.2(ENSG00000253496):​n.279-4364A>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 0.904 in 152,214 control chromosomes in the GnomAD database, including 62,798 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 0.90 (62798 hom., cov: 32)
• Consequence: ENST00000521411.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379297	XR_949525.1	n.158-4364A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521411.2	n.279-4364A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137541 AN: 152096 Hom.: 62783 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.904 AC: 137604 AN: 152214 Hom.: 62798 Cov.: 32 AF XY: 0.904 AC XY: 67303 AN XY: 74418

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.928

Alfa AF: 0.928 Hom.: 8192

Bravo AF: 0.896

Asia WGS AF: 0.903 AC: 3140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6992112; hg19: chr8-16645155;