rs7925637

Positions:

• chr11-87493416-G-A
• chr11-87493416-G-T

Variant summary

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

The XR_002957260.2(LOC107984361):​n.396-59883G>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 0.279 in 151,914 control chromosomes in the GnomAD database, including 6,848 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 0.28 (6848 hom., cov: 32)
• Consequence: LOC107984361 XR_002957260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

LOC107984361 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984361	XR_002957260.2	n.396-59883G>A		intron_variant, non_coding_transcript_variant
LOC107984361	XR_001748316.2	n.319-59883G>A		intron_variant, non_coding_transcript_variant
LOC107984361	XR_002957261.2	n.319-59883G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42365 AN: 151796 Hom.: 6829 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.279 AC: 42423 AN: 151914 Hom.: 6848 Cov.: 32 AF XY: 0.280 AC XY: 20822 AN XY: 74264

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.239

Alfa AF: 0.221 Hom.: 1876

Bravo AF: 0.282

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7925637; hg19: chr11-87204458;