2-60436663-C-T

Variant names:

• chr2-60436663-C-T
• rs8179712
• XM_047446573.1:c.331+2609G>A

Variant summary

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

The XM_047446573.1(LOC124906010):​c.331+2609G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,144 control chromosomes in the GnomAD database, including 2,841 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 0.14 (2841 hom., cov: 32)
• Consequence: LOC124906010 XM_047446573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

Genes affected

LOC124906010 (HGNC:):

MIR4432HG (HGNC:52005): (MIR4432 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906010	XM_047446573.1	c.331+2609G>A		intron_variant	Intron 2 of 2		XP_047302529.1
LOC124906010	XR_007086328.1	n.497+977G>A		intron_variant	Intron 3 of 5
LOC124906010	XR_007086329.1	n.422+2609G>A		intron_variant	Intron 2 of 4
LOC124906010	XR_007086331.1	n.256+2901G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000650395.1	n.265+2901G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22029 AN: 152026 Hom.: 2830 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.145 AC: 22059 AN: 152144 Hom.: 2841 Cov.: 32 AF XY: 0.159 AC XY: 11790 AN XY: 74382

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0947 Hom.: 1656

Bravo AF: 0.155

Asia WGS AF: 0.460 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8179712; hg19: chr2-60663798;