1-194339198-T-G

Variant summary

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

The XR_001738356.2(LOC107985242):n.312+15107A>C 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 0.94 in 152,058 control chromosomes in the GnomAD database, including 67,491 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 0.94 (67491 hom., cov: 33)
• Consequence: LOC107985242 XR_001738356.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

Genes affected

LOC107985242 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985242	XR_001738356.2	n.312+15107A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.941 AC: 142915 AN: 151940 Hom.: 67473 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.940 AC: 142987 AN: 152058 Hom.: 67491 Cov.: 33 AF XY: 0.942 AC XY: 70062 AN XY: 74352

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.949

Alfa AF: 0.953 Hom.: 8594

Bravo AF: 0.935

Asia WGS AF: 0.968 AC: 3343 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.12
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6663592; hg19: chr1-194308328;