10-43807771-T-C

Position:

• chr10-43807771-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659335.1(LINC00840):​n.1025+10899T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,052 control chromosomes in the GnomAD database, including 14,384 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 0.43 (14384 hom., cov: 33)
• Consequence: LINC00840 ENST00000659335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

Genes affected

LINC00840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378275	XR_945906.4	n.1026-10736T>C		intron_variant
LOC105378275	XR_945907.2	n.179-10736T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00840	ENST00000659335.1	n.1025+10899T>C		intron_variant
LINC00840	ENST00000666323.1	n.1010+10899T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64937 AN: 151932 Hom.: 14355 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.427 AC: 65000 AN: 152052 Hom.: 14384 Cov.: 33 AF XY: 0.425 AC XY: 31614 AN XY: 74338

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.423

Alfa AF: 0.398 Hom.: 24807

Bravo AF: 0.449

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7922745; hg19: chr10-44303219;