7-55015669-C-T

Position:

• chr7-55015669-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.2362+892G>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 0.244 in 152,076 control chromosomes in the GnomAD database, including 5,718 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 0.24 (5718 hom., cov: 32)
• Consequence: LOC105375284 XR_007060329.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

LOC105375284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375284	XR_007060329.1	n.2362+892G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37029 AN: 151958 Hom.: 5718 Cov.: 32

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.244 AC: 37038 AN: 152076 Hom.: 5718 Cov.: 32 AF XY: 0.251 AC XY: 18654 AN XY: 74338

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.223

Alfa AF: 0.261 Hom.: 1213

Bravo AF: 0.237

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
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: rs12674036; hg19: chr7-55083362;