7-127553613-A-G

Position:

• chr7-127553613-A-G

Variant summary

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

The XR_007060511.1(LOC105375490):​n.92-18382T>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 0.609 in 152,082 control chromosomes in the GnomAD database, including 28,877 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 0.61 (28877 hom., cov: 32)
• Consequence: LOC105375490 XR_007060511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375490	XR_007060511.1	n.92-18382T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92475 AN: 151964 Hom.: 28829 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.609 AC: 92573 AN: 152082 Hom.: 28877 Cov.: 32 AF XY: 0.613 AC XY: 45562 AN XY: 74358

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.562

Alfa AF: 0.583 Hom.: 4436

Bravo AF: 0.602

Asia WGS AF: 0.714 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.9
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: rs11761076; hg19: chr7-127193667;