rs10233157

Positions:

• chr7-26086909-G-A
• chr7-26086909-G-T

Variant summary

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

The XR_927114.3(LOC105375199):​n.159-17108C>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 0.108 in 151,202 control chromosomes in the GnomAD database, including 2,267 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 0.11 (2267 hom., cov: 32)
• Consequence: LOC105375199 XR_927114.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

LOC105375199 (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 = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375199	XR_927114.3	n.159-17108C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16251 AN: 151084 Hom.: 2266 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.00851

Gnomad OTH AF: 0.0857

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

GnomAD4 genome AF: 0.108 AC: 16277 AN: 151202 Hom.: 2267 Cov.: 32 AF XY: 0.107 AC XY: 7923 AN XY: 73804

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.00851

Gnomad4 OTH AF: 0.0852

Alfa AF: 0.0487 Hom.: 231

Bravo AF: 0.120

Asia WGS AF: 0.163 AC: 568 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	0.22
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10233157; hg19: chr7-26126529;