rs346062

chr19-43694425-G-A

Variant summary

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

The NR_172891.1(LOC105372412):n.965-625G>A 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 0.613 in 152,006 control chromosomes in the GnomAD database, including 29,045 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 0.61 (29045 hom., cov: 31)
• Consequence: LOC105372412 NR_172891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372412	NR_172891.1	n.965-625G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000636801.1	n.299-625G>A		intron_variant, non_coding_transcript_variant
	ENST00000637093.1	n.139-625G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93051 AN: 151888 Hom.: 29015 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.613 AC: 93134 AN: 152006 Hom.: 29045 Cov.: 31 AF XY: 0.612 AC XY: 45474 AN XY: 74312

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.594

Alfa AF: 0.599 Hom.: 4699

Bravo AF: 0.613

Asia WGS AF: 0.551 AC: 1918 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	0.0050
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346062; hg19: chr19-44198577;