rs714023

Positions:

• chr22-30909855-G-A

Variant summary

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

The NR_146603.1(LOC107985544):​n.326+1443C>T 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 0.096 in 152,186 control chromosomes in the GnomAD database, including 983 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 0.096 (983 hom., cov: 33)
• Consequence: LOC107985544 NR_146603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

LOC107985544 (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 (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985544	NR_146603.1	n.326+1443C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14616 AN: 152068 Hom.: 983 Cov.: 33

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0960 AC: 14607 AN: 152186 Hom.: 983 Cov.: 33 AF XY: 0.0953 AC XY: 7087 AN XY: 74390

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.122 Hom.: 841

Bravo AF: 0.0857

Asia WGS AF: 0.0230 AC: 79 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	0.16
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714023; hg19: chr22-31305842;