10-78742102-C-T

Position:

• chr10-78742102-C-T

Variant summary

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

The XR_946100.2(LOC105378379):​n.446+1996G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,102 control chromosomes in the GnomAD database, including 40,529 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 0.71 (40529 hom., cov: 32)
• Consequence: LOC105378379 XR_946100.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

Genes affected

LOC105378379 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378379	XR_946100.2	n.446+1996G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107599 AN: 151984 Hom.: 40545 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.707 AC: 107612 AN: 152102 Hom.: 40529 Cov.: 32 AF XY: 0.705 AC XY: 52415 AN XY: 74362

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.714

Alfa AF: 0.805 Hom.: 28826

Bravo AF: 0.698

Asia WGS AF: 0.720 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35648; hg19: chr10-80501859;