rs7068990

Positions:

• chr10-120329400-G-A
• chr10-120329400-G-C

Variant summary

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

The XR_001747606.1(LOC105378515):​n.994-7121G>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 0.229 in 151,178 control chromosomes in the GnomAD database, including 4,299 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 0.23 (4299 hom., cov: 31)
• Consequence: LOC105378515 XR_001747606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

Genes affected

LOC105378515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378515	XR_001747606.1	n.994-7121G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34544 AN: 151062 Hom.: 4295 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34555 AN: 151178 Hom.: 4299 Cov.: 31 AF XY: 0.237 AC XY: 17551 AN XY: 73926

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.221

Alfa AF: 0.233 Hom.: 2272

Bravo AF: 0.205

Asia WGS AF: 0.291 AC: 1009 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7068990; hg19: chr10-122088912;