19-19362636-T-C

Position:

• chr19-19362636-T-C

Variant summary

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

The XR_007067163.1(LOC124904656):​n.482-3675A>G 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 0.572 in 151,760 control chromosomes in the GnomAD database, including 26,124 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 0.57 (26124 hom., cov: 30)
• Consequence: LOC124904656 XR_007067163.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC124904656 (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 (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904656	XR_007067163.1	n.482-3675A>G		intron_variant, non_coding_transcript_variant
LOC124904656	XR_007067161.1	n.119-3675A>G		intron_variant, non_coding_transcript_variant
LOC124904656	XR_007067162.1	n.93+45A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86763 AN: 151642 Hom.: 26131 Cov.: 30

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.572 AC: 86755 AN: 151760 Hom.: 26124 Cov.: 30 AF XY: 0.574 AC XY: 42594 AN XY: 74170

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.566

Alfa AF: 0.586 Hom.: 5632

Bravo AF: 0.551

Asia WGS AF: 0.542 AC: 1885 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	0.77
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2905424; hg19: chr19-19473445;