rs879048

Variant names:

• chr11-27617387-C-A
• rs879048
• ENST00000499008.8:n.214-22458C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-27617387-C-A
• chr11-27617387-C-T

Variant summary

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

The ENST00000527083.6(LINC00678):​n.1233G>T 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 0.736 in 152,018 control chromosomes in the GnomAD database, including 41,811 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 0.74 (41811 hom., cov: 31)
• Consequence: LINC00678 ENST00000527083.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 16 publications found

Genes affected

BDNF-AS (HGNC:20608): (BDNF antisense RNA)

LINC00678 (HGNC:44413): (long intergenic non-protein coding RNA 678)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527083.6. 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
	BDNF-AS	NR_002832.2		n.214-22458C>A		intron	N/A
	BDNF-AS	NR_033312.1		n.145-22458C>A		intron	N/A
	BDNF-AS	NR_033313.1		n.145-22458C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.214-22458C>A		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.145-22458C>A		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.145-22458C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111730 AN: 151898 Hom.: 41769 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.736 AC: 111827 AN: 152018 Hom.: 41811 Cov.: 31 AF XY: 0.737 AC XY: 54791 AN XY: 74326

African (AFR) AF: 0.621 AC: 25716 AN: 41436

American (AMR) AF: 0.786 AC: 12000 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2530 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2668 AN: 5148

South Asian (SAS) AF: 0.738 AC: 3545 AN: 4806

European-Finnish (FIN) AF: 0.840 AC: 8906 AN: 10598

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.795 AC: 54065 AN: 67976

Other (OTH) AF: 0.745 AC: 1573 AN: 2110

Alfa AF: 0.714 Hom.: 10119

Bravo AF: 0.725

Asia WGS AF: 0.684 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.59
PhyloP100		-0.42

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: rs879048;

hg19: chr11-27638934;