chr7-112607132-C-T

Variant names:

• chr7-112607132-C-T
• rs43083
• ENST00000777765.1:n.267-13276C>T

Variant summary

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

The ENST00000777765.1(LINC03076):​n.267-13276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,102 control chromosomes in the GnomAD database, including 48,992 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 0.79 (48992 hom., cov: 32)
• Consequence: LINC03076 ENST00000777765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 3 publications found

Genes affected

LINC03076 (HGNC:56656): (long intergenic non-protein coding RNA 3076)

ENSG00000301323 (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 (AFR) allele frequency at 95% confidence interval = 0.873 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
LINC03076	ENST00000777765.1	n.267-13276C>T		intron_variant	Intron 2 of 2
LINC03076	ENST00000777766.1	n.388-13276C>T		intron_variant	Intron 1 of 1
ENSG00000301323	ENST00000778011.1	n.219-9763G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120349 AN: 151984 Hom.: 48935 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.792 AC: 120466 AN: 152102 Hom.: 48992 Cov.: 32 AF XY: 0.783 AC XY: 58199 AN XY: 74362

African (AFR) AF: 0.880 AC: 36541 AN: 41520

American (AMR) AF: 0.649 AC: 9900 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2933 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1223 AN: 5150

South Asian (SAS) AF: 0.663 AC: 3190 AN: 4810

European-Finnish (FIN) AF: 0.806 AC: 8527 AN: 10574

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55471 AN: 68002

Other (OTH) AF: 0.808 AC: 1706 AN: 2112

Alfa AF: 0.806 Hom.: 135000

Bravo AF: 0.785

Asia WGS AF: 0.539 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.40
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs43083; hg19: chr7-112247187;