rs3913061

Positions:

• chr12-58551492-G-A
• chr12-58551492-G-C

Variant summary

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

The ENST00000546977.5(ENSG00000258231):​n.56+7313G>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 0.662 in 152,106 control chromosomes in the GnomAD database, including 33,409 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 0.66 (33409 hom., cov: 33)
• Consequence: ENST00000546977.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369789	XR_945007.3	n.666-330C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000546977.5	n.56+7313G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100639 AN: 151988 Hom.: 33391 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.662 AC: 100712 AN: 152106 Hom.: 33409 Cov.: 33 AF XY: 0.661 AC XY: 49115 AN XY: 74338

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.670

Alfa AF: 0.673 Hom.: 4274

Bravo AF: 0.662

Asia WGS AF: 0.662 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3913061; hg19: chr12-58945275;