rs6664825

chr1-55973656-A-Cchr1-55973656-A-G

Variant summary

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

The XR_007067029.1(LOC105378737):n.297+11667A>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 0.265 in 150,936 control chromosomes in the GnomAD database, including 5,257 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 0.27 (5257 hom., cov: 32)
• Consequence: LOC105378737 XR_007067029.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740

Genes affected

LOC105378737 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378737	XR_007067029.1	n.297+11667A>C		intron_variant, non_coding_transcript_variant
LOC105378737	XR_001738068.2	n.298-1672A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646266.1	n.465-1672A>C		intron_variant, non_coding_transcript_variant
	ENST00000661225.1	n.293-1672A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.265 AC: 39999 AN: 150824 Hom.: 5247 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.265 AC: 40031 AN: 150936 Hom.: 5257 Cov.: 32 AF XY: 0.265 AC XY: 19535 AN XY: 73804

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.288

Alfa AF: 0.212 Hom.: 881

Bravo AF: 0.264

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.67
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6664825; hg19: chr1-56439329;