rs780873

chr12-115757976-G-Achr12-115757976-G-T

Variant summary

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

The ENST00000549163.1(ENSG00000257781):n.129+2586G>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 0.939 in 152,232 control chromosomes in the GnomAD database, including 67,205 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 0.94 (67205 hom., cov: 32)
• Consequence: ENST00000549163.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

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 = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370003	XR_945389.3	n.118+4972C>T		intron_variant, non_coding_transcript_variant
LOC105370003	XR_945388.3	n.118+4972C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000549163.1	n.129+2586G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142822 AN: 152114 Hom.: 67157 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.939 AC: 142928 AN: 152232 Hom.: 67205 Cov.: 32 AF XY: 0.940 AC XY: 69973 AN XY: 74436

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.937

Alfa AF: 0.948 Hom.: 101372

Bravo AF: 0.937

Asia WGS AF: 0.978 AC: 3399 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	4.6
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780873; hg19: chr12-116195781;