rs1946663

chr12-93935900-G-Achr12-93935900-G-T

Variant summary

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

The NR_135017.1(LOC105369911):n.62+7645C>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 0.422 in 152,002 control chromosomes in the GnomAD database, including 13,732 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 0.42 (13732 hom., cov: 32)
• Consequence: LOC105369911 NR_135017.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369911	NR_135017.1	n.62+7645C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000550687.1	n.59+7645C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64155 AN: 151884 Hom.: 13733 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.422 AC: 64174 AN: 152002 Hom.: 13732 Cov.: 32 AF XY: 0.420 AC XY: 31202 AN XY: 74280

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.427

Alfa AF: 0.410 Hom.: 25027

Bravo AF: 0.433

Asia WGS AF: 0.379 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1946663; hg19: chr12-94329676;