7-127529843-C-T

Position:

• chr7-127529843-C-T

Variant summary

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

The XR_007060511.1(LOC105375490):​n.174+5306G>A 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 0.475 in 151,954 control chromosomes in the GnomAD database, including 19,387 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 0.47 (19387 hom., cov: 32)
• Consequence: LOC105375490 XR_007060511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375490	XR_007060511.1	n.174+5306G>A		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745351.2	n.2291+5306G>A		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745352.2	n.493+5306G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72072 AN: 151838 Hom.: 19366 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.475 AC: 72114 AN: 151954 Hom.: 19387 Cov.: 32 AF XY: 0.484 AC XY: 35959 AN XY: 74268

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.450

Alfa AF: 0.517 Hom.: 2971

Bravo AF: 0.448

Asia WGS AF: 0.684 AC: 2376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10282411; hg19: chr7-127169897;