rs17884563

Positions:

• chr7-95400715-T-A

Variant summary

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

The XR_007060439.1(LOC107986822):​n.557+3687T>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 0.068 in 152,038 control chromosomes in the GnomAD database, including 471 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 0.068 (471 hom., cov: 31)
• Consequence: LOC107986822 XR_007060439.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

LOC107986822 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986822	XR_007060439.1	n.557+3687T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10336 AN: 151920 Hom.: 473 Cov.: 31

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0680 AC: 10332 AN: 152038 Hom.: 471 Cov.: 31 AF XY: 0.0661 AC XY: 4912 AN XY: 74278

Gnomad4 AFR AF: 0.0173

Gnomad4 AMR AF: 0.0736

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.0456

Gnomad4 NFE AF: 0.0933

Gnomad4 OTH AF: 0.0744

Alfa AF: 0.0773 Hom.: 76

Bravo AF: 0.0695

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17884563; hg19: chr7-95030027;