chr19-35433855-C-T

Position:

• chr19-35433855-C-T

Variant summary

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

The XR_935947.3(LOC101927522):​n.848G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,156 control chromosomes in the GnomAD database, including 5,881 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 0.27 (5877 hom., cov: 32)
  • Exomes 𝑓: 0.48 (4 hom.)
• Consequence: LOC101927522 XR_935947.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

LOC101927522 (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 = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927522	XR_935947.3	n.848G>A		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000428426.2	n.610-22G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41358 AN: 151994 Hom.: 5867 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.477 AC: 21 AN: 44 Hom.: 4 Cov.: 0 AF XY: 0.500 AC XY: 15 AN XY: 30

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.475

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.272 AC: 41412 AN: 152112 Hom.: 5877 Cov.: 32 AF XY: 0.275 AC XY: 20444 AN XY: 74356

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.274

Alfa AF: 0.264 Hom.: 3089

Bravo AF: 0.269

Asia WGS AF: 0.387 AC: 1347 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	0.19
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2312305; hg19: chr19-35924757;