chr19-41641662-G-C

Position:

• chr19-41641662-G-C

Variant summary

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

The XR_935972.1(LOC105372405):​n.367C>G 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 0.211 in 152,142 control chromosomes in the GnomAD database, including 3,715 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 0.21 (3715 hom., cov: 32)
• Consequence: LOC105372405 XR_935972.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

LOC105372405 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372405	XR_935972.1	n.367C>G		non_coding_transcript_exon_variant	3/3
		n.41641662G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32103 AN: 152024 Hom.: 3715 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.211 AC: 32106 AN: 152142 Hom.: 3715 Cov.: 32 AF XY: 0.205 AC XY: 15231 AN XY: 74376

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.00578

Gnomad4 SAS AF: 0.0997

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.228

Alfa AF: 0.128 Hom.: 240

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015758; hg19: chr19-42148030;