rs2881814

chr7-7324759-A-Gchr7-7324759-A-T

Variant summary

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

The XR_002956539.2(LOC107986764):n.442-51802A>G 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 0.742 in 152,100 control chromosomes in the GnomAD database, including 42,673 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 0.74 (42673 hom., cov: 32)
• Consequence: LOC107986764 XR_002956539.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

Genes affected

LOC107986764 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986764	XR_002956539.2	n.442-51802A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112839 AN: 151982 Hom.: 42641 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.742 AC: 112924 AN: 152100 Hom.: 42673 Cov.: 32 AF XY: 0.750 AC XY: 55780 AN XY: 74350

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.746

Alfa AF: 0.763 Hom.: 7556

Bravo AF: 0.731

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.52
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2881814; hg19: chr7-7364390;