rs775448

chr12-69723630-G-A

Variant summary

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

The NR_110072.2(LOC101928002):n.565+1592C>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 0.32 in 152,008 control chromosomes in the GnomAD database, including 8,193 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 0.32 (8193 hom., cov: 31)
• Consequence: LOC101928002 NR_110072.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928002	NR_110072.2	n.565+1592C>T		intron_variant, non_coding_transcript_variant
LOC101928002	NR_159971.1	n.442-1059C>T		intron_variant, non_coding_transcript_variant
LOC101928002	NR_159972.1	n.441+1592C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501387.6	n.589+1592C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000501300.1	n.454-1059C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000661191.1	n.441+1592C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48668 AN: 151890 Hom.: 8190 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.320 AC: 48674 AN: 152008 Hom.: 8193 Cov.: 31 AF XY: 0.323 AC XY: 23992 AN XY: 74298

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.306

Alfa AF: 0.358 Hom.: 4782

Bravo AF: 0.302

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.3
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs775448; hg19: chr12-70117410;