rs17402905

Positions:

• chr2-60433173-T-C
• chr2-60433173-T-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+6099A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,108 control chromosomes in the GnomAD database, including 4,093 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 0.22 (4093 hom., cov: 32)
• Consequence: LOC124906010 XM_047446573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

LOC124906010 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906010	XM_047446573.1	c.331+6099A>G		intron_variant			XP_047302529.1
LOC124906010	XR_007086328.1	n.606+280A>G		intron_variant
LOC124906010	XR_007086329.1	n.531+280A>G		intron_variant
LOC124906010	XR_007086331.1	n.365+280A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000650395.1	n.265+6391A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33043 AN: 151990 Hom.: 4096 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.217 AC: 33035 AN: 152108 Hom.: 4093 Cov.: 32 AF XY: 0.212 AC XY: 15750 AN XY: 74352

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.180

Alfa AF: 0.179 Hom.: 711

Bravo AF: 0.204

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17402905; hg19: chr2-60660308;