chr10-31100384-A-T

Variant names:

• chr10-31100384-A-T
• rs867992
• ENST00000658872.1:n.323-5555A>T

Variant summary

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

The ENST00000658872.1(LINC02664):​n.323-5555A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,124 control chromosomes in the GnomAD database, including 14,228 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 0.40 (14228 hom., cov: 33)
• Consequence: LINC02664 ENST00000658872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16
• Publications: 2 publications found

Genes affected

LINC02664 (HGNC:54150): (long intergenic non-protein coding RNA 2664)

LOC105376481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376481	XR_001747409.3	n.2795-5555A>T		intron_variant	Intron 1 of 2
LOC105376481	XR_001747410.3	n.2795-5555A>T		intron_variant	Intron 1 of 2
LOC105376481	XR_930796.3	n.904-5555A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000658872.1	n.323-5555A>T		intron_variant	Intron 1 of 2
LINC02664	ENST00000804994.1	n.91-5555A>T		intron_variant	Intron 1 of 3
LINC02664	ENST00000805304.1	n.212-5555A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61046 AN: 152006 Hom.: 14228 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.401 AC: 61052 AN: 152124 Hom.: 14228 Cov.: 33 AF XY: 0.406 AC XY: 30231 AN XY: 74376

African (AFR) AF: 0.157 AC: 6535 AN: 41502

American (AMR) AF: 0.457 AC: 6976 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3466

East Asian (EAS) AF: 0.397 AC: 2053 AN: 5176

South Asian (SAS) AF: 0.364 AC: 1758 AN: 4824

European-Finnish (FIN) AF: 0.616 AC: 6512 AN: 10566

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34471 AN: 67992

Other (OTH) AF: 0.369 AC: 781 AN: 2114

Alfa AF: 0.462 Hom.: 2196

Bravo AF: 0.378

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.55
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs867992; hg19: chr10-31389313;