rs6992708

Variant names:

• chr8-81492914-T-C
• rs6992708
• ENST00000524085.2:n.299-5003T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524085.2(ENSG00000253374):​n.299-5003T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,040 control chromosomes in the GnomAD database, including 10,713 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 0.36 (10713 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 2 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.517+30940T>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.299-5003T>C		intron_variant	Intron 2 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-28793T>C		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-28793T>C		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-28793T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54091 AN: 151922 Hom.: 10683 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.356 AC: 54175 AN: 152040 Hom.: 10713 Cov.: 32 AF XY: 0.353 AC XY: 26234 AN XY: 74342

African (AFR) AF: 0.497 AC: 20597 AN: 41450

American (AMR) AF: 0.342 AC: 5222 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 987 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3588 AN: 5158

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4824

European-Finnish (FIN) AF: 0.204 AC: 2157 AN: 10588

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19234 AN: 67968

Other (OTH) AF: 0.348 AC: 733 AN: 2106

Alfa AF: 0.353 Hom.: 1530

Bravo AF: 0.378

Asia WGS AF: 0.491 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.061
DANN	Benign	0.52
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6992708; hg19: chr8-82405149;