rs2215564

Positions:

• chr7-150866876-T-C

Variant summary

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

The XR_928171.3(LOC105375567):​n.122+10133A>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 0.087 in 152,272 control chromosomes in the GnomAD database, including 734 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 0.087 (734 hom., cov: 33)
• Consequence: LOC105375567 XR_928171.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

LOC105375567 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375567	XR_928171.3	n.122+10133A>G		intron_variant, non_coding_transcript_variant
LOC105375567	XR_928169.3	n.122+10133A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13243 AN: 152154 Hom.: 733 Cov.: 33

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0870 AC: 13242 AN: 152272 Hom.: 734 Cov.: 33 AF XY: 0.0855 AC XY: 6365 AN XY: 74470

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.0812

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.0832

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.116 Hom.: 1457

Bravo AF: 0.0826

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215564; hg19: chr7-150563964;