rs7070369

Positions:

• chr10-86756209-G-A
• chr10-86756209-G-C
• chr10-86756209-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000608826.1(ENSG00000272631):​n.90C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,980 control chromosomes in the GnomAD database, including 7,637 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.29 (7630 hom., cov: 32)
  • Exomes 𝑓: 0.70 (7 hom.)
• Consequence: ENST00000608826.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP6: Variant 10-86756209-G-A is Benign according to our data. Variant chr10-86756209-G-A is described in ClinVar as [Benign]. Clinvar id is 1229698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86756209-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMPR1A	NM_001406562.1	c.-373+105G>A		intron_variant			NP_001393491.1
BMPR1A	NM_001406564.1	c.-373+246G>A		intron_variant			NP_001393493.1
BMPR1A	NM_001406566.1	c.-268+246G>A		intron_variant			NP_001393495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000608826.1	n.90C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43948 AN: 151834 Hom.: 7629 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.700 AC: 21 AN: 30 Hom.: 7 Cov.: 0 AF XY: 0.750 AC XY: 15 AN XY: 20

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.708

GnomAD4 genome AF: 0.289 AC: 43955 AN: 151950 Hom.: 7630 Cov.: 32 AF XY: 0.296 AC XY: 21997 AN XY: 74286

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.292

Alfa AF: 0.313 Hom.: 1376

Bravo AF: 0.278

Asia WGS AF: 0.433 AC: 1502 AN: 3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.4
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: rs7070369; hg19: chr10-88515966;