rs692842

Variant names:

• chr11-64391211-C-T
• rs692842
• ENST00000757243.1:n.212-3175C>T

Variant summary

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

The ENST00000757243.1(ENSG00000298679):​n.212-3175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 150,964 control chromosomes in the GnomAD database, including 20,528 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 0.52 (20528 hom., cov: 29)
• Consequence: ENSG00000298679 ENST00000757243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 5 publications found

Genes affected

ENSG00000298679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298679	ENST00000757243.1	n.212-3175C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78161 AN: 150846 Hom.: 20509 Cov.: 29

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.518 AC: 78212 AN: 150964 Hom.: 20528 Cov.: 29 AF XY: 0.513 AC XY: 37829 AN XY: 73690

African (AFR) AF: 0.471 AC: 19381 AN: 41116

American (AMR) AF: 0.476 AC: 7241 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1687 AN: 3458

East Asian (EAS) AF: 0.350 AC: 1794 AN: 5124

South Asian (SAS) AF: 0.498 AC: 2383 AN: 4782

European-Finnish (FIN) AF: 0.500 AC: 5191 AN: 10374

Middle Eastern (MID) AF: 0.500 AC: 145 AN: 290

European-Non Finnish (NFE) AF: 0.573 AC: 38758 AN: 67640

Other (OTH) AF: 0.539 AC: 1124 AN: 2086

Alfa AF: 0.534 Hom.: 2735

Bravo AF: 0.516

Asia WGS AF: 0.416 AC: 1438 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs692842; hg19: chr11-64158683;