XM_047449400.1:c.*338+232A>C

Variant names:

• chr3-30605914-T-G
• rs11466480
• XM_047449400.1:c.*338+232A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XM_047449400.1(LOC105377015):​c.*338+232A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 152,316 control chromosomes in the GnomAD database, including 26 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 0.015 (26 hom., cov: 32)
• Consequence: LOC105377015 XM_047449400.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

LOC105377015 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0154 (2346/152316) while in subpopulation NFE AF= 0.0268 (1822/68024). AF 95% confidence interval is 0.0258. There are 26 homozygotes in gnomad4. There are 1016 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377015	XM_047449400.1	c.*338+232A>C		intron_variant	Intron 1 of 1		XP_047305356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0154 AC: 2345 AN: 152196 Hom.: 26 Cov.: 32

Gnomad AFR AF: 0.00483

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.00608

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000620

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0154 AC: 2346 AN: 152316 Hom.: 26 Cov.: 32 AF XY: 0.0136 AC XY: 1016 AN XY: 74484

Gnomad4 AFR AF: 0.00484

Gnomad4 AMR AF: 0.00608

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000621

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0268

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.0197 Hom.: 9

Bravo AF: 0.0149

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11466480; hg19: chr3-30647406;