rs10487140

chr7-95695829-G-A

Variant summary

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

The XR_927774.3(LOC105375409):n.177-21278G>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 0.194 in 151,436 control chromosomes in the GnomAD database, including 3,096 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 0.19 (3096 hom., cov: 32)
• Consequence: LOC105375409 XR_927774.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

LOC105375409 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375409	XR_927774.3	n.177-21278G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29326 AN: 151318 Hom.: 3096 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.194 AC: 29319 AN: 151436 Hom.: 3096 Cov.: 32 AF XY: 0.194 AC XY: 14346 AN XY: 73966

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.190

Alfa AF: 0.210 Hom.: 6859

Bravo AF: 0.188

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487140; hg19: chr7-95325141;