chr10-102869116-A-G

Position:

• chr10-102869116-A-G

Variant summary

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

The NR_037644.1(BORCS7-ASMT):​n.407-689A>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 0.355 in 152,092 control chromosomes in the GnomAD database, including 9,796 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 0.35 (9796 hom., cov: 32)
• Consequence: BORCS7-ASMT NR_037644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

Genes affected

BORCS7-ASMT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BORCS7-ASMT	NR_037644.1	n.407-689A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53935 AN: 151974 Hom.: 9788 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.355 AC: 53982 AN: 152092 Hom.: 9796 Cov.: 32 AF XY: 0.353 AC XY: 26243 AN XY: 74346

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.368

Alfa AF: 0.355 Hom.: 17811

Bravo AF: 0.362

Asia WGS AF: 0.374 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085104; hg19: chr10-104628873;