rs6782380

Positions:

• chr3-55150186-C-G

Variant summary

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

The XR_007095917.1(LOC124906243):​n.159-6264G>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 0.168 in 152,056 control chromosomes in the GnomAD database, including 2,222 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 0.17 (2222 hom., cov: 33)
• Consequence: LOC124906243 XR_007095917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

LOC124906243 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906243	XR_007095917.1	n.159-6264G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25520 AN: 151938 Hom.: 2215 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.168 AC: 25566 AN: 152056 Hom.: 2222 Cov.: 33 AF XY: 0.162 AC XY: 12067 AN XY: 74302

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0982

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.177

Alfa AF: 0.162 Hom.: 265

Bravo AF: 0.171

Asia WGS AF: 0.129 AC: 450 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	0.43
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6782380; hg19: chr3-55184213;