chr19-41137939-T-C

Position:

• chr19-41137939-T-C

Variant summary

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

The XM_047439802.1(LOC124904790):​c.185-515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,092 control chromosomes in the GnomAD database, including 52,027 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 0.82 (52027 hom., cov: 31)
• Consequence: LOC124904790 XM_047439802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

LOC124904790 (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 (AMR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904790	XM_047439802.1	c.185-515A>G		intron_variant			XP_047295758.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124979 AN: 151974 Hom.: 51983 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.822 AC: 125080 AN: 152092 Hom.: 52027 Cov.: 31 AF XY: 0.827 AC XY: 61496 AN XY: 74358

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.843

Alfa AF: 0.837 Hom.: 9676

Bravo AF: 0.813

Asia WGS AF: 0.883 AC: 3070 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	1.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1631931; hg19: chr19-41643844;