rs12668127

chr7-127508578-G-Achr7-127508578-G-T

Variant summary

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

The XR_007060511.1(LOC105375490):n.232+603C>T 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 0.325 in 152,044 control chromosomes in the GnomAD database, including 10,067 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 0.32 (10067 hom., cov: 32)
• Consequence: LOC105375490 XR_007060511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375490	XR_007060511.1	n.232+603C>T		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745351.2	n.2349+603C>T		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745352.2	n.551+603C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49340 AN: 151926 Hom.: 10055 Cov.: 32

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.325 AC: 49351 AN: 152044 Hom.: 10067 Cov.: 32 AF XY: 0.333 AC XY: 24760 AN XY: 74322

Gnomad4 AFR AF: 0.0903

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.324

Alfa AF: 0.374 Hom.: 12236

Bravo AF: 0.308

Asia WGS AF: 0.506 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.067
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12668127; hg19: chr7-127148632;