chr7-55017274-C-T

Position:

• chr7-55017274-C-T

Variant summary

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

The XR_007060329.1(LOC105375284):​n.1649G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 152,246 control chromosomes in the GnomAD database, including 189 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 0.040 (189 hom., cov: 33)
• Consequence: LOC105375284 XR_007060329.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

Genes affected

LOC105375284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375284	XR_007060329.1	n.1649G>A		non_coding_transcript_exon_variant	1/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6128 AN: 152132 Hom.: 188 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0403 AC: 6138 AN: 152246 Hom.: 189 Cov.: 33 AF XY: 0.0402 AC XY: 2995 AN XY: 74414

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.0562

Gnomad4 FIN AF: 0.0358

Gnomad4 NFE AF: 0.0388

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0375 Hom.: 69

Bravo AF: 0.0405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6965469; hg19: chr7-55084967;