3-61428140-C-G

Position:

• chr3-61428140-C-G

Variant summary

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

The XR_001740725.2(LOC105377114):​n.202+374G>C 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 0.0668 in 152,114 control chromosomes in the GnomAD database, including 425 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 0.067 (425 hom., cov: 31)
• Consequence: LOC105377114 XR_001740725.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396

Genes affected

LOC105377114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377114	XR_001740725.2	n.202+374G>C		intron_variant, non_coding_transcript_variant
LOC105377114	XR_940892.3	n.202+374G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10142 AN: 151996 Hom.: 424 Cov.: 31

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.0599

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0668 AC: 10165 AN: 152114 Hom.: 425 Cov.: 31 AF XY: 0.0706 AC XY: 5248 AN XY: 74350

Gnomad4 AFR AF: 0.0850

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0554

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.0482

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0520 Hom.: 147

Bravo AF: 0.0646

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514718; hg19: chr3-61413814;