chr7-127524904-A-G

Position:

• chr7-127524904-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.174+10245T>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 0.556 in 151,988 control chromosomes in the GnomAD database, including 24,182 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 0.56 (24182 hom., cov: 32)
• Consequence: LOC105375490 XR_007060511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375490	XR_007060511.1	n.174+10245T>C		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745351.2	n.2291+10245T>C		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745352.2	n.493+10245T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84447 AN: 151870 Hom.: 24130 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.556 AC: 84548 AN: 151988 Hom.: 24182 Cov.: 32 AF XY: 0.559 AC XY: 41524 AN XY: 74290

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.517

Alfa AF: 0.523 Hom.: 9976

Bravo AF: 0.555

Asia WGS AF: 0.635 AC: 2202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
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: rs6467136; hg19: chr7-127164958;