7-26544101-G-T

Position:

• chr7-26544101-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007060263.1(LOC124901605):​n.803C>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 0.12 in 152,250 control chromosomes in the GnomAD database, including 1,211 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 0.12 (1211 hom., cov: 33)
• Consequence: LOC124901605 XR_007060263.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

LOC124901605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901605	XR_007060263.1	n.803C>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18206 AN: 152132 Hom.: 1208 Cov.: 33

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.120 AC: 18215 AN: 152250 Hom.: 1211 Cov.: 33 AF XY: 0.122 AC XY: 9057 AN XY: 74434

Gnomad4 AFR AF: 0.0611

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0551

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.110

Alfa AF: 0.133 Hom.: 1486

Bravo AF: 0.109

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17284017; hg19: chr7-26583720; COSMIC: COSV53495504;