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 ENST00000832857.1(ENSG00000253374):​n.327-28793T>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 ENST00000832857.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253374	ENST00000524085.2	TSL:5	n.299-5003T>C		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.327-28793T>C		intron	N/A
	ENSG00000253374	ENST00000832858.1		n.309-28793T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6992708;

hg19: chr8-82405149;