19-41167943-G-T

Position:

• chr19-41167943-G-T

Variant summary

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

The XM_047439802.1(LOC124904790):​c.184+8016C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,028 control chromosomes in the GnomAD database, including 3,560 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 0.18 (3560 hom., cov: 31)
• Consequence: LOC124904790 XM_047439802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

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 (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904790	XM_047439802.1	c.184+8016C>A		intron_variant			XP_047295758.1
		n.41167943G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26583 AN: 151910 Hom.: 3542 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0927

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.175 AC: 26640 AN: 152028 Hom.: 3560 Cov.: 31 AF XY: 0.173 AC XY: 12831 AN XY: 74328

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.0790

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0555

Gnomad4 NFE AF: 0.0927

Gnomad4 OTH AF: 0.162

Alfa AF: 0.103 Hom.: 2314

Bravo AF: 0.200

Asia WGS AF: 0.104 AC: 362 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	0.39
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8105815; hg19: chr19-41673848;