rs1117702

Positions:

• chr7-9855925-G-A
• chr7-9855925-G-C
• chr7-9855925-G-T

Variant summary

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

The XR_927026.2(LOC105375147):​n.209+10865C>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 0.217 in 152,010 control chromosomes in the GnomAD database, including 3,825 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 0.22 (3825 hom., cov: 32)
• Consequence: LOC105375147 XR_927026.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

LOC105375147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375147	XR_927026.2	n.209+10865C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32958 AN: 151890 Hom.: 3826 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.217 AC: 32960 AN: 152010 Hom.: 3825 Cov.: 32 AF XY: 0.218 AC XY: 16210 AN XY: 74302

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.199

Alfa AF: 0.133 Hom.: 336

Bravo AF: 0.203

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1117702; hg19: chr7-9895554;