rs2159222

Positions:

• chr7-15718375-A-T

Variant summary

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

The XR_927057.3(LOC101927558):​n.854+565A>T 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 0.137 in 152,160 control chromosomes in the GnomAD database, including 1,961 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 0.14 (1961 hom., cov: 32)
• Consequence: LOC101927558 XR_927057.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

Genes affected

LOC101927558 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927558	XR_927057.3	n.854+565A>T		intron_variant, non_coding_transcript_variant
LOC101927558	XR_001745101.2	n.859+565A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20781 AN: 152042 Hom.: 1963 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.137 AC: 20787 AN: 152160 Hom.: 1961 Cov.: 32 AF XY: 0.141 AC XY: 10500 AN XY: 74392

Gnomad4 AFR AF: 0.0338

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0766

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.136

Alfa AF: 0.143 Hom.: 245

Bravo AF: 0.134

Asia WGS AF: 0.215 AC: 747 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2159222; hg19: chr7-15758000;