rs1011407

Positions:

• chr2-60438633-A-G

Variant summary

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

The XM_047446573.1(LOC124906010):​c.331+639T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 152,330 control chromosomes in the GnomAD database, including 593 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 0.076 (593 hom., cov: 32)
• Consequence: LOC124906010 XM_047446573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

LOC124906010 (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 (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906010	XM_047446573.1	c.331+639T>C		intron_variant			XP_047302529.1
LOC124906010	XM_047446574.1	c.331+639T>C		intron_variant			XP_047302530.1
LOC124906010	XR_007086328.1	n.422+639T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000650395.1	n.265+931T>C		intron_variant
MIR4432HG	ENST00000686152.1	n.260-919T>C		intron_variant
MIR4432HG	ENST00000692549.1	n.429+639T>C		intron_variant
MIR4432HG	ENST00000702294.1	n.410+648T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11573 AN: 152212 Hom.: 592 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.0759 AC: 11569 AN: 152330 Hom.: 593 Cov.: 32 AF XY: 0.0727 AC XY: 5414 AN XY: 74492

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0362

Gnomad4 FIN AF: 0.0778

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.104 Hom.: 408

Bravo AF: 0.0742

Asia WGS AF: 0.0210 AC: 72 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	2.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011407; hg19: chr2-60665768;