rs3087465

Positions:

• chr3-30605668-A-G
• chr3-30605668-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XM_047449400.1(LOC105377015):​c.*339-110T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,138 control chromosomes in the GnomAD database, including 34,469 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.64 (34469 hom., cov: 32)
• Consequence: LOC105377015 XM_047449400.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0860

Genes affected

LOC105377015 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 3-30605668-A-G is Benign according to our data. Variant chr3-30605668-A-G is described in ClinVar as [Benign]. Clinvar id is 1167240.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377015	XM_047449400.1	c.*339-110T>C		intron_variant			XP_047305356.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98063 AN: 152020 Hom.: 34464 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.645 AC: 98087 AN: 152138 Hom.: 34469 Cov.: 32 AF XY: 0.646 AC XY: 48067 AN XY: 74358

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.668

Alfa AF: 0.751 Hom.: 42201

Bravo AF: 0.628

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial thoracic aortic aneurysm and aortic dissection Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3087465; hg19: chr3-30647160;