7-55018519-A-C

Position:

• chr7-55018519-A-C

Variant summary

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

The XR_007060329.1(LOC105375284):​n.404T>G 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 0.853 in 152,136 control chromosomes in the GnomAD database, including 55,417 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 0.85 (55417 hom., cov: 32)
• Consequence: LOC105375284 XR_007060329.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LOC105375284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375284	XR_007060329.1	n.404T>G		non_coding_transcript_exon_variant	1/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129697 AN: 152018 Hom.: 55390 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.853 AC: 129779 AN: 152136 Hom.: 55417 Cov.: 32 AF XY: 0.852 AC XY: 63340 AN XY: 74358

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.877

Alfa AF: 0.854 Hom.: 8320

Bravo AF: 0.851

Asia WGS AF: 0.949 AC: 3300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs759171; hg19: chr7-55086212; COSMIC: COSV51842751;