7-11914949-A-G

Position:

• chr7-11914949-A-G

Variant summary

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

The XR_007060211.1(LOC124901589):​n.86-21563T>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 0.178 in 152,162 control chromosomes in the GnomAD database, including 2,547 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 0.18 (2547 hom., cov: 32)
• Consequence: LOC124901589 XR_007060211.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

Genes affected

LOC124901589 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901589	XR_007060211.1	n.86-21563T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27131 AN: 152044 Hom.: 2547 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.178 AC: 27149 AN: 152162 Hom.: 2547 Cov.: 32 AF XY: 0.181 AC XY: 13480 AN XY: 74376

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.189

Alfa AF: 0.181 Hom.: 3519

Bravo AF: 0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10234648; hg19: chr7-11954575;