rs7095665

chr10-85544742-G-Achr10-85544742-G-T

Variant summary

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

The XR_946157.3(LOC105378404):n.3338-4515C>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 0.52 in 151,930 control chromosomes in the GnomAD database, including 20,843 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 0.52 (20843 hom., cov: 32)
• Consequence: LOC105378404 XR_946157.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

LOC105378404 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378404	XR_946157.3	n.3338-4515C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78947 AN: 151812 Hom.: 20832 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.520 AC: 79003 AN: 151930 Hom.: 20843 Cov.: 32 AF XY: 0.518 AC XY: 38462 AN XY: 74228

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.552

Alfa AF: 0.549 Hom.: 10444

Bravo AF: 0.522

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.67
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7095665; hg19: chr10-87304499;